Explanation and inference: mechanistic and functional explanations guide property generalization.

Science.gov (United States)

Lombrozo, Tania; Gwynne, Nicholas Z

2014-01-01

The ability to generalize from the known to the unknown is central to learning and inference. Two experiments explore the relationship between how a property is explained and how that property is generalized to novel species and artifacts. The experiments contrast the consequences of explaining a property mechanistically, by appeal to parts and processes, with the consequences of explaining the property functionally, by appeal to functions and goals. The findings suggest that properties that are explained functionally are more likely to be generalized on the basis of shared functions, with a weaker relationship between mechanistic explanations and generalization on the basis of shared parts and processes. The influence of explanation type on generalization holds even though all participants are provided with the same mechanistic and functional information, and whether an explanation type is freely generated (Experiment 1), experimentally provided (Experiment 2), or experimentally induced (Experiment 2). The experiments also demonstrate that explanations and generalizations of a particular type (mechanistic or functional) can be experimentally induced by providing sample explanations of that type, with a comparable effect when the sample explanations come from the same domain or from a different domains. These results suggest that explanations serve as a guide to generalization, and contribute to a growing body of work supporting the value of distinguishing mechanistic and functional explanations.

Comparative ecophysiology of two sympatric lizards. Laying the groundwork for mechanistic distribution models

Directory of Open Access Journals (Sweden)

Enrique García-Muñoz

2013-12-01

Full Text Available Distribution modelling usually makes inferences correlating species presence and environmental variables but does not take biotic relations into account. Alternative approaches based on a mechanistic understanding of biological processes are now being applied. Regarding lacertid lizards, physiological traits such as preferred body temperature (Tp are well known to correlate with several physiological optima. Much less is known about their water ecology although body temperature and evaporative water loss (Wl may trade-off. Two saxicolous lacertids, Algyroides marchi and Podarcis hispanica ss are sympatric in the Subbetic Mountains (SE Spain were they can be found in syntopy. Previous distribution modelling indicates the first species is associated with mountains, low temperatures; high precipitation and forest cover whereas the second one is more generalistic. Here, we perform two ecophysiological tests with both species: a Tp experiment in thermal gradient and a Wl experiment in sealed chambers. Although both species attained similar body temperatures, A. marchi lost more water and more uniformly in time than P. hispanica ss that displayed an apparent response to dehydration. These results suggest that water loss rather temperature is crucial to explain the distribution patterns of A. marchi in relation to P. hispanica ss, the former risking dehydration in dry areas no matter what temperature is. Ecophysiological traits represent a promising tool to build future mechanistic models for (lacertid lizards. Additionally, the implications for their biogeography and conservation are discussed.

Assessing uncertainty in mechanistic models

Science.gov (United States)

Edwin J. Green; David W. MacFarlane; Harry T. Valentine

2000-01-01

Concern over potential global change has led to increased interest in the use of mechanistic models for predicting forest growth. The rationale for this interest is that empirical models may be of limited usefulness if environmental conditions change. Intuitively, we expect that mechanistic models, grounded as far as possible in an understanding of the biology of tree...

Regulatory Technology Development Plan - Sodium Fast Reactor: Mechanistic Source Term - Trial Calculation

International Nuclear Information System (INIS)

Grabaskas, David

2016-01-01

The potential release of radioactive material during a plant incident, referred to as the source term, is a vital design metric and will be a major focus of advanced reactor licensing. The U.S. Nuclear Regulatory Commission has stated an expectation for advanced reactor vendors to present a mechanistic assessment of the potential source term in their license applications. The mechanistic source term presents an opportunity for vendors to realistically assess the radiological consequences of an incident, and may allow reduced emergency planning zones and smaller plant sites. However, the development of a mechanistic source term for advanced reactors is not without challenges, as there are often numerous phenomena impacting the transportation and retention of radionuclides. This project sought to evaluate U.S. capabilities regarding the mechanistic assessment of radionuclide release from core damage incidents at metal fueled, pool-type sodium fast reactors (SFRs). The purpose of the analysis was to identify, and prioritize, any gaps regarding computational tools or data necessary for the modeling of radionuclide transport and retention phenomena. To accomplish this task, a parallel-path analysis approach was utilized. One path, led by Argonne and Sandia National Laboratories, sought to perform a mechanistic source term assessment using available codes, data, and models, with the goal to identify gaps in the current knowledge base. The second path, performed by an independent contractor, performed sensitivity analyses to determine the importance of particular radionuclides and transport phenomena in regards to offsite consequences. The results of the two pathways were combined to prioritize gaps in current capabilities.

Comparative analysis of a LOCA for a German PWR with ASTEC and ATHLET-CD

International Nuclear Information System (INIS)

Reinke, N.; Chan, H.W.; Sonnenkalb, M.

2013-01-01

This paper presents the results of a comparative analysis performed with ASTEC V2.02 and a coupled ATHLET-CD V2.2c /COCOSYS V2.4 calculation for a German 1300 MWe KONVOI type PWR. The purpose of this analysis is mainly to assess the ASTEC code behaviour in modelling of both the thermal-hydraulic phenomena in the coolant circuit arising during a hypothetical severe accident and the early phase of the core degradation versus the more mechanistic code system ATHLET-CD/COCOSYS. The performed analyses cover a loss of coolant accident sequence (LOCA). Such comparison has been done for the first time. The integral code ASTEC (Accident Source Term Evaluation Code) commonly developed since 1996 by IRSN and GRS is a fast running programme, which allows the calculation of entire sequences of severe accidents (SA) in light water reactors from the initiating event up to the release of fission products into the environment, thereby covering all important in-vessel and containment phenomena. The thermal-hydraulic mechanistic system code ATHLET (Analysis of THermal-hydraulics of LEaks and Transients) is being developed by GRS for the analysis of the whole spectrum of leaks and transients in PWRs and BWRs. For modeling of core degradation processes the CD part (Core Degradation) of ATHLET can be activated. For analyses of the containment behavior, ATHLET-CD has been coupled to the GRS code COCOSYS (COntainment COde SYStem). (orig.)

Proceedings of the international workshop on mechanistic understanding of radionuclide migration in compacted/intact systems

International Nuclear Information System (INIS)

Tachi, Yukio; Yui, Mikazu

2010-03-01

The international workshop on mechanistic understanding of radionuclide migration in compacted / intact systems was held at ENTRY, JAEA, Tokai on 21st - 23rd January, 2009. This workshop was hosted by Japan Atomic Energy Agency (JAEA) as part of the project on the mechanistic model/database development for radionuclide sorption and diffusion behavior in compacted / intact systems. The overall goal of the project is to develop the mechanistic model / database for a consistent understanding and prediction of migration parameters and its uncertainties for performance assessment of geological disposal of radioactive waste. The objective of the workshop is to integrate the state-of-the-art of mechanistic sorption and diffusion model in compacted / intact systems, especially in bentonite / clay systems, and discuss the JAEA's mechanistic approaches and future challenges, especially the following discussions points; 1) What's the status and difficulties for mechanistic model/database development? 2) What's the status and difficulties for applicability of mechanistic model to the compacted/intact system? 3) What's the status and difficulties for obtaining evidences for mechanistic model? 4) What's the status and difficulties for standardization of experimental methodology for batch sorption and diffusion? 5) What's the uncertainties of transport parameters in radionuclides migration analysis due to a lack of understanding/experimental methodologies, and how do we derive them? This report includes workshop program, overview and materials of each presentation, summary of discussions. (author)

Regulatory Technology Development Plan - Sodium Fast Reactor: Mechanistic Source Term – Trial Calculation

Energy Technology Data Exchange (ETDEWEB)

Grabaskas, David [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Bucknor, Matthew [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Jerden, James [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Brunett, Acacia J. [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Denman, Matthew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Nuclear Engineering Division; Clark, Andrew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Nuclear Engineering Division; Denning, Richard S. [Consultant, Columbus, OH (United States)

2016-10-01

The potential release of radioactive material during a plant incident, referred to as the source term, is a vital design metric and will be a major focus of advanced reactor licensing. The U.S. Nuclear Regulatory Commission has stated an expectation for advanced reactor vendors to present a mechanistic assessment of the potential source term in their license applications. The mechanistic source term presents an opportunity for vendors to realistically assess the radiological consequences of an incident, and may allow reduced emergency planning zones and smaller plant sites. However, the development of a mechanistic source term for advanced reactors is not without challenges, as there are often numerous phenomena impacting the transportation and retention of radionuclides. This project sought to evaluate U.S. capabilities regarding the mechanistic assessment of radionuclide release from core damage incidents at metal fueled, pool-type sodium fast reactors (SFRs). The purpose of the analysis was to identify, and prioritize, any gaps regarding computational tools or data necessary for the modeling of radionuclide transport and retention phenomena. To accomplish this task, a parallel-path analysis approach was utilized. One path, led by Argonne and Sandia National Laboratories, sought to perform a mechanistic source term assessment using available codes, data, and models, with the goal to identify gaps in the current knowledge base. The second path, performed by an independent contractor, performed sensitivity analyses to determine the importance of particular radionuclides and transport phenomena in regards to offsite consequences. The results of the two pathways were combined to prioritize gaps in current capabilities.

A preliminary study of mechanistic approach in pavement design to accommodate climate change effects

Science.gov (United States)

Harnaeni, S. R.; Pramesti, F. P.; Budiarto, A.; Setyawan, A.

2018-03-01

Road damage is caused by some factors, including climate changes, overload, and inappropriate procedure for material and development process. Meanwhile, climate change is a phenomenon which cannot be avoided. The effects observed include air temperature rise, sea level rise, rainfall changes, and the intensity of extreme weather phenomena. Previous studies had shown the impacts of climate changes on road damage. Therefore, several measures to anticipate the damage should be considered during the planning and construction in order to reduce the cost of road maintenance. There are three approaches generally applied in the design of flexible pavement thickness, namely mechanistic approach, mechanistic-empirical (ME) approach and empirical approach. The advantages of applying mechanistic approach or mechanistic-empirical (ME) approaches are its efficiency and reliability in the design of flexible pavement thickness as well as its capacity to accommodate climate changes in compared to empirical approach. However, generally, the design of flexible pavement thickness in Indonesia still applies empirical approach. This preliminary study aimed to emphasize the importance of the shifting towards a mechanistic approach in the design of flexible pavement thickness.

Appropriateness of mechanistic and non-mechanistic models for the application of ultrafiltration to mixed waste

International Nuclear Information System (INIS)

Foust, Henry; Ghosehajra, Malay

2007-01-01

This study asks two questions: (1) How appropriate is the use of a basic filtration equation to the application of ultrafiltration of mixed waste, and (2) How appropriate are non-parametric models for permeate rates (volumes)? To answer these questions, mechanistic and non-mechanistic approaches are developed for permeate rates and volumes associated with an ultrafiltration/mixed waste system in dia-filtration mode. The mechanistic approach is based on a filtration equation which states that t/V vs. V is a linear relationship. The coefficients associated with this linear regression are composed of physical/chemical parameters of the system and based the mass balance equation associated with the membrane and associated developing cake layer. For several sets of data, a high correlation is shown that supports the assertion that t/V vs. V is a linear relationship. It is also shown that non-mechanistic approaches, i.e., the use of regression models to are not appropriate. One models considered is Q(p) = a*ln(Cb)+b. Regression models are inappropriate because the scale-up from a bench scale (pilot scale) study to full-scale for permeate rates (volumes) is not simply the ratio of the two membrane surface areas. (authors)

Rational and Mechanistic Perspectives on Reinforcement Learning

Science.gov (United States)

Chater, Nick

2009-01-01

This special issue describes important recent developments in applying reinforcement learning models to capture neural and cognitive function. But reinforcement learning, as a theoretical framework, can apply at two very different levels of description: "mechanistic" and "rational." Reinforcement learning is often viewed in mechanistic terms--as…

Controls on the spatial variability of key soil properties: comparing field data with a mechanistic soilscape evolution model

Science.gov (United States)

Vanwalleghem, T.; Román, A.; Giraldez, J. V.

2016-12-01

There is a need for better understanding the processes influencing soil formation and the resulting distribution of soil properties. Soil properties can exhibit strong spatial variation, even at the small catchment scale. Especially soil carbon pools in semi-arid, mountainous areas are highly uncertain because bulk density and stoniness are very heterogeneous and rarely measured explicitly. In this study, we explore the spatial variability in key soil properties (soil carbon stocks, stoniness, bulk density and soil depth) as a function of processes shaping the critical zone (weathering, erosion, soil water fluxes and vegetation patterns). We also compare the potential of a geostatistical versus a mechanistic soil formation model (MILESD) for predicting these key soil properties. Soil core samples were collected from 67 locations at 6 depths. Total soil organic carbon stocks were 4.38 kg m-2. Solar radiation proved to be the key variable controlling soil carbon distribution. Stone content was mostly controlled by slope, indicating the importance of erosion. Spatial distribution of bulk density was found to be highly random. Finally, total carbon stocks were predicted using a random forest model whose main covariates were solar radiation and NDVI. The model predicts carbon stocks that are double as high on north versus south-facing slopes. However, validation showed that these covariates only explained 25% of the variation in the dataset. Apparently, present-day landscape and vegetation properties are not sufficient to fully explain variability in the soil carbon stocks in this complex terrain under natural vegetation. This is attributed to a high spatial variability in bulk density and stoniness, key variables controlling carbon stocks. Similar results were obtained with the mechanistic soil formation model MILESD, suggesting that more complex models might be needed to further explore this high spatial variability.

Analysis of WWER-440 and PWR RPV welds surveillance data to compare irradiation damage evolution

Energy Technology Data Exchange (ETDEWEB)

Debarberis, L. [Joint Research Centre of the European Commission, Institute for Energy, P.O. Box 2, 1755 ZG Petten (Netherlands)]. E-mail: luigi.debarberis@cec.eu.int; Acosta, B. [Joint Research Centre of the European Commission, Institute for Energy, P.O. Box 2, 1755 ZG Petten (Netherlands)]. E-mail: beatriz.acosta-iborra@jrc.nl; Zeman, A. [Joint Research Centre of the European Commission, Institute for Energy, P.O. Box 2, 1755 ZG Petten (Netherlands); Sevini, F. [Joint Research Centre of the European Commission, Institute for Energy, P.O. Box 2, 1755 ZG Petten (Netherlands); Ballesteros, A. [Tecnatom, Avd. Montes de Oca 1, San Sebasitan de los Reyes, E-28709 Madrid (Spain); Kryukov, A. [Russian Research Centre Kurchatov Institute, Kurchatov Square 1, 123182 Moscow (Russian Federation); Gillemot, F. [AEKI Atomic Research Institute, Konkoly Thege M. ut 29-33, 1121 Budapest (Hungary); Brumovsky, M. [NRI, Nuclear Research Institute, Husinec-Rez 130, 25068 Rez (Czech Republic)

2006-04-15

It is known that for Russian-type and Western water reactor pressure vessel steels there is a similar degradation in mechanical properties during equivalent neutron irradiation. Available surveillance results from WWER and PWR vessels are used in this article to compare irradiation damage evolution for the different reactor pressure vessel welds. The analysis is done through the semi-mechanistic model for radiation embrittlement developed by JRC-IE. Consistency analysis with BWR vessel materials and model alloys has also been performed within this study. Globally the two families of studied materials follow similar trends regarding the evolution of irradiation damage. Moreover in the high fluence range typical of operation of WWER the radiation stability of these vessels is greater than the foreseen one for PWR.

Proposed key characteristics of male reproductive toxicants as a method for organizing and screening mechanistic evidence for non-cancer outcomes.

Science.gov (United States)

The adoption of systematic review practices for risk assessment includes integration of evidence obtained from experimental, epidemiological, and mechanistic studies. Although mechanistic evidence plays an important role in mode of action analysis, the process of sorting and anal...

Evaluation of mechanistic DNB models using HCLWR CHF data

International Nuclear Information System (INIS)

Iwamura, Takamichi; Watanabe, Hironori; Okubo, Tsutomu; Araya, Fumimasa; Murao, Yoshio.

1992-03-01

An onset of departure from nucleate boiling (DNB) in light water reactor (LWR) has been generally predicted with empirical correlations. Since these correlations have less physical bases and contain adjustable empirical constants determined by best fitting of test data, applicable geometries and flow conditions are limited within the original experiment ranges. In order to obtain more universal prediction method, several mechanistic DNB models based on physical approaches have been proposed in recent years. However, the predictive capabilities of mechanistic DNB models have not been verified successfully especially for advanced LWR design purposes. In this report, typical DNB mechanistic models are reviewed and compared with critical heat flux (CHF) data for high conversion light water reactor (HCLWR). The experiments were performed using triangular 7-rods array with non-uniform axial heat flux distribution. Test pressure was 16 MPa, mass velocities ranged from 800 t0 3100 kg/s·m 2 and exit qualities from -0.07 to 0.19. The evaluated models are: 1) Wisman-Pei, 2) Chang-Lee, 3) Lee-Mudawwar, 4) Lin-Lee-Pei, and 5) Katto. The first two models are based on near-wall bubble crowding model and the other three models on sublayer dryout model. The comparison with experimental data indicated that the Weisman-Pei model agreed relatively well with the CHF data. Effects of empirical constants in each model on CHF calculation were clarified by sensitivity studies. It was also found that the magnitudes of physical quantities obtained in the course of calculation were significantly different for each model. Therefore, microscopic observation of the onset of DNB on heated surface is essential to clarify the DNB mechanism and establish a general DNB mechanistic model based on physical phenomenon. (author)

Mechanistic curiosity will not kill the Bayesian cat

NARCIS (Netherlands)

Borsboom, D.; Wagenmakers, E.-J.; Romeijn, J.-W.

2011-01-01

Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

Mechanistic curiosity will not kill the Bayesian cat

NARCIS (Netherlands)

Borsboom, Denny; Wagenmakers, Eric-Jan; Romeijn, Jan-Willem

Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

Calibrating mechanistic-empirical pavement performance models with an expert matrix

Energy Technology Data Exchange (ETDEWEB)

Tighe, S.; AlAssar, R.; Haas, R. [Waterloo Univ., ON (Canada). Dept. of Civil Engineering; Zhiwei, H. [Stantec Consulting Ltd., Cambridge, ON (Canada)

2001-07-01

Proper management of pavement infrastructure requires pavement performance modelling. For the past 20 years, the Ontario Ministry of Transportation has used the Ontario Pavement Analysis of Costs (OPAC) system for pavement design. Pavement needs, however, have changed substantially during that time. To address this need, a new research contract is underway to enhance the model and verify the predictions, particularly at extreme points such as low and high traffic volume pavement design. This initiative included a complete evaluation of the existing OPAC pavement design method, the construction of a new set of pavement performance prediction models, and the development of the flexible pavement design procedure that incorporates reliability analysis. The design was also expanded to include rigid pavement designs and modification of the existing life cycle cost analysis procedure which includes both the agency cost and road user cost. Performance prediction and life-cycle costs were developed based on several factors, including material properties, traffic loads and climate. Construction and maintenance schedules were also considered. The methodology for the calibration and validation of a mechanistic-empirical flexible pavement performance model was described. Mechanistic-empirical design methods combine theory based design such as calculated stresses, strains or deflections with empirical methods, where a measured response is associated with thickness and pavement performance. Elastic layer analysis was used to determine pavement response to determine the most effective design using cumulative Equivalent Single Axle Loads (ESALs), below grade type and layer thickness.The new mechanistic-empirical model separates the environment and traffic effects on performance. This makes it possible to quantify regional differences between Southern and Northern Ontario. In addition, roughness can be calculated in terms of the International Roughness Index or Riding comfort Index

Numerical simulation in steam injection process by a mechanistic approach

Energy Technology Data Exchange (ETDEWEB)

De Souza, J.C.Jr.; Campos, W.; Lopes, D.; Moura, L.S.S. [Petrobras, Rio de Janeiro (Brazil)

2008-10-15

Steam injection is a common thermal recovery method used in very viscous oil reservoirs. The method involves the injection of heat to reduce viscosity and mobilize oil. A steam generation and injection system consists primarily of a steam source, distribution lines, injection wells and a discarding tank. In order to optimize injection and improve the oil recovery factor, one must determine the parameters of steam flow such as pressure, temperature and steam quality. This study focused on developing a unified mathematical model by means of a mechanistic approach for two-phase steam flow in pipelines and wells. The hydrodynamic and heat transfer mechanistic model was implemented in a computer simulator to model the parameters of steam injection while trying to avoid the use of empirical correlations. A marching algorithm was used to determine the distribution of pressure and temperature along the pipelines and wellbores. The mathematical model for steam flow in injection systems, developed by a mechanistic approach (VapMec) performed well when the simulated values of pressures and temperatures were compared with the values measured during field tests. The newly developed VapMec model was incorporated in the LinVap-3 simulator that constitutes an engineering supporting tool for steam injection wells operated by Petrobras. 23 refs., 7 tabs., 6 figs.

Modeling and validation of a mechanistic tool (MEFISTO) for the prediction of critical power in BWR fuel assemblies

International Nuclear Information System (INIS)

Adamsson, Carl; Le Corre, Jean-Marie

2011-01-01

Highlights: → The MEFISTO code efficiently and accurately predicts the dryout event in a BWR fuel bundle, using a mechanistic model. → A hybrid approach between a fast and robust sub-channel analysis and a three-field two-phase analysis is adopted. → MEFISTO modeling approach, calibration, CPU usage, sensitivity, trend analysis and performance evaluation are presented. → The calibration parameters and process were carefully selected to preserve the mechanistic nature of the code. → The code dryout prediction performance is near the level of fuel-specific empirical dryout correlations. - Abstract: Westinghouse is currently developing the MEFISTO code with the main goal to achieve fast, robust, practical and reliable prediction of steady-state dryout Critical Power in Boiling Water Reactor (BWR) fuel bundle based on a mechanistic approach. A computationally efficient simulation scheme was used to achieve this goal, where the code resolves all relevant field (drop, steam and multi-film) mass balance equations, within the annular flow region, at the sub-channel level while relying on a fast and robust two-phase (liquid/steam) sub-channel solution to provide the cross-flow information. The MEFISTO code can hence provide highly detailed solution of the multi-film flow in BWR fuel bundle while enhancing flexibility and reducing the computer time by an order of magnitude as compared to a standard three-field sub-channel analysis approach. Models for the numerical computation of the one-dimensional field flowrate distributions in an open channel (e.g. a sub-channel), including the numerical treatment of field cross-flows, part-length rods, spacers grids and post-dryout conditions are presented in this paper. The MEFISTO code is then applied to dryout prediction in BWR fuel bundle using VIPRE-W as a fast and robust two-phase sub-channel driver code. The dryout power is numerically predicted by iterating on the bundle power so that the minimum film flowrate in the

Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

Science.gov (United States)

MacLeod, Miles; Nersessian, Nancy J

2015-02-01

In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.

Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation

Directory of Open Access Journals (Sweden)

Mathavan Sinnakaruppan

2010-03-01

Full Text Available Abstract Background Mercury is a prominent environmental contaminant that causes detrimental effects to human health. Although the liver has been known to be a main target organ, there is limited information on in vivo molecular mechanism of mercury-induced toxicity in the liver. By using transcriptome analysis, phenotypic anchoring and validation of targeted gene expression in zebrafish, mercury-induced hepatotoxicity was investigated and a number of perturbed cellular processes were identified and compared with those captured in the in vitro human cell line studies. Results Hepato-transcriptome analysis of mercury-exposed zebrafish revealed that the earliest deregulated genes were associated with electron transport chain, mitochondrial fatty acid beta-oxidation, nuclear receptor signaling and apoptotic pathway, followed by complement system and proteasome pathway, and thereafter DNA damage, hypoxia, Wnt signaling, fatty acid synthesis, gluconeogenesis, cell cycle and motility. Comparative meta-analysis of microarray data between zebrafish liver and human HepG2 cells exposed to mercury identified some common toxicological effects of mercury-induced hepatotoxicity in both models. Histological analyses of liver from mercury-exposed fish revealed morphological changes of liver parenchyma, decreased nucleated cell count, increased lipid vesicles, glycogen and apoptotic bodies, thus providing phenotypic evidence for anchoring of the transcriptome analysis. Validation of targeted gene expression confirmed deregulated gene-pathways from enrichment analysis. Some of these genes responding to low concentrations of mercury may serve as toxicogenomic-based markers for detection and health risk assessment of environmental mercury contaminations. Conclusion Mercury-induced hepatotoxicity was triggered by oxidative stresses, intrinsic apoptotic pathway, deregulation of nuclear receptor and kinase activities including Gsk3 that deregulates Wnt signaling

Mechanistic Analysis of Cocrystal Dissolution as a Function of pH and Micellar Solubilization.

Science.gov (United States)

Cao, Fengjuan; Amidon, Gordon L; Rodriguez-Hornedo, Nair; Amidon, Gregory E

2016-03-07

The purpose of this work is to provide a mechanistic understanding of the dissolution behavior of cocrystals under the influence of ionization and micellar solubilization. Mass transport models were developed by applying Fick's law of diffusion to dissolution with simultaneous chemical reactions in the hydrodynamic boundary layer adjacent to the dissolving cocrystal surface to predict the pH at the dissolving solid-liquid interface (i.e., interfacial pH) and the flux of cocrystals. To evaluate the predictive power of these models, dissolution studies of carbamazepine-saccharin (CBZ-SAC) and carbamazepine-salicylic acid (CBZ-SLC) cocrystals were performed at varied pH and surfactant concentrations above the critical stabilization concentration (CSC), where the cocrystals were thermodynamically stable. The findings in this work demonstrate that the pH dependent dissolution behavior of cocrystals with ionizable components is dependent on interfacial pH. This mass transport analysis demonstrates the importance of pH, cocrystal solubility, diffusivity, and micellar solubilization on the dissolution rates of cocrystals.

Comparative approaches from empirical to mechanistic simulation modelling in Land Evaluation studies

Science.gov (United States)

Manna, P.; Basile, A.; Bonfante, A.; Terribile, F.

2009-04-01

The Land Evaluation (LE) comprise the evaluation procedures to asses the attitudes of the land to a generic or specific use (e.g. biomass production). From local to regional and national scale the approach to the land use planning should requires a deep knowledge of the processes that drive the functioning of the soil-plant-atmosphere system. According to the classical approaches the assessment of attitudes is the result of a qualitative comparison between the land/soil physical properties and the land use requirements. These approaches have a quick and inexpensive applicability; however, they are based on empirical and qualitative models with a basic knowledge structure specifically built for a specific landscape and for the specific object of the evaluation (e.g. crop). The outcome from this situation is the huge difficulties in the spatial extrapolation of the LE results and the rigidity of the system. Modern techniques instead, rely on the application of mechanistic and quantitative simulation modelling that allow a dynamic characterisation of the interrelated physical and chemical processes taking place in the soil landscape. Moreover, the insertion of physical based rules in the LE procedure may make it less difficult in terms of both extending spatially the results and changing the object (e.g. crop species, nitrate dynamics, etc.) of the evaluation. On the other side these modern approaches require high quality and quantity of input data that cause a significant increase in costs. In this scenario nowadays the LE expert is asked to choose the best LE methodology considering costs, complexity of the procedure and benefits in handling a specific land evaluation. In this work we performed a forage maize land suitability study by comparing 9 different methods having increasing complexity and costs. The study area, of about 2000 ha, is located in North Italy in the Lodi plain (Po valley). The range of the 9 employed methods ranged from standard LE approaches to

Causation at Different Levels: Tracking the Commitments of Mechanistic Explanations

DEFF Research Database (Denmark)

Fazekas, Peter; Kertész, Gergely

2011-01-01

connections transparent. These general commitments get confronted with two claims made by certain proponents of the mechanistic approach: William Bechtel often argues that within the mechanistic framework it is possible to balance between reducing higher levels and maintaining their autonomy at the same time...... their autonomy at the same time than standard reductive accounts are, and that what mechanistic explanations are able to do at best is showing that downward causation does not exist....

LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

Directory of Open Access Journals (Sweden)

Rasmus Magnusson

2017-06-01

Full Text Available Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM, which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE for gene regulatory networks (GRNs. LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models

Application of mechanistic models to fermentation and biocatalysis for next-generation processes

DEFF Research Database (Denmark)

Gernaey, Krist; Eliasson Lantz, Anna; Tufvesson, Pär

2010-01-01

of variables required for measurement, control and process design. In the near future, mechanistic models with a higher degree of detail will play key roles in the development of efficient next-generation fermentation and biocatalytic processes. Moreover, mechanistic models will be used increasingly......Mechanistic models are based on deterministic principles, and recently, interest in them has grown substantially. Herein we present an overview of mechanistic models and their applications in biotechnology, including future perspectives. Model utility is highlighted with respect to selection...

Mechanistic Basis of Cocrystal Dissolution Advantage.

Science.gov (United States)

Cao, Fengjuan; Amidon, Gordon L; Rodríguez-Hornedo, Naír; Amidon, Gregory E

2018-01-01

Current interest in cocrystal development resides in the advantages that the cocrystal may have in solubility and dissolution compared with the parent drug. This work provides a mechanistic analysis and comparison of the dissolution behavior of carbamazepine (CBZ) and its 2 cocrystals, carbamazepine-saccharin (CBZ-SAC) and carbamazepine-salicylic acid (CBZ-SLC) under the influence of pH and micellar solubilization. A simple mathematical equation is derived based on the mass transport analyses to describe the dissolution advantage of cocrystals. The dissolution advantage is the ratio of the cocrystal flux to drug flux and is defined as the solubility advantage (cocrystal to drug solubility ratio) times the diffusivity advantage (cocrystal to drug diffusivity ratio). In this work, the effective diffusivity of CBZ in the presence of surfactant was determined to be different and less than those of the cocrystals. The higher effective diffusivity of drug from the dissolved cocrystals, the diffusivity advantage, can impart a dissolution advantage to cocrystals with lower solubility than the parent drug while still maintaining thermodynamic stability. Dissolution conditions where cocrystals can display both thermodynamic stability and a dissolution advantage can be obtained from the mass transport models, and this information is useful for both cocrystal selection and formulation development. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Numerical simulation in steam injection wellbores by mechanistic approach; Simulacao numerica do escoamento de vapor em pocos por uma abordagem mecanicista

Energy Technology Data Exchange (ETDEWEB)

Souza Junior, J.C. de; Campos, W.; Lopes, D.; Moura, L.S.S. [PETROBRAS, Rio de Janeiro, RJ (Brazil); Thomas, A. Clecio F. [Universidade Estadual do Ceara (UECE), CE (Brazil)

2008-07-01

This work addresses to the development of a hydrodynamic and heat transfer mechanistic model for steam flow in injection wellbores. The problem of two-phase steam flow in wellbores has been solved recently by using available empirical correlations from petroleum industry (Lopes, 1986) and nuclear industry (Moura, 1991).The good performance achieved by mechanistic models developed by Ansari (1994), Hasan (1995), Gomez (2000) and Kaya (2001) supports the importance of the mechanistic approach for the steam flow problem in injection wellbores. In this study, the methodology to solve the problem consists in the application of a numerical method to the governing equations of steam flow and a marching algorithm to determine the distribution of the pressure and temperature along the wellbore. So, a computer code has been formulated to get numerical results, which provides a comparative study to the main models found in the literature. Finally, when compared to available field data, the mechanistic model for downward vertical steam flow in wellbores gave better results than the empirical correlations. (author)

Assessing Metal Levels in Children from the Mechanistic Indicators of Childhood Asthma(MICA) study

Science.gov (United States)

Toxic and essential metals levels can be used as health indicators. Here, we quantitatively compare and contrast toxic and essential metals levels in vacuum dust, urine, and fingernail samples of 109 children in Detroit, Michigan as part of The Mechanistic Indicators of Childhood...

Uncertainty, sensitivity analysis and the role of data based mechanistic modeling in hydrology

Science.gov (United States)

Ratto, M.; Young, P. C.; Romanowicz, R.; Pappenberger, F.; Saltelli, A.; Pagano, A.

2007-05-01

In this paper, we discuss a joint approach to calibration and uncertainty estimation for hydrologic systems that combines a top-down, data-based mechanistic (DBM) modelling methodology; and a bottom-up, reductionist modelling methodology. The combined approach is applied to the modelling of the River Hodder catchment in North-West England. The top-down DBM model provides a well identified, statistically sound yet physically meaningful description of the rainfall-flow data, revealing important characteristics of the catchment-scale response, such as the nature of the effective rainfall nonlinearity and the partitioning of the effective rainfall into different flow pathways. These characteristics are defined inductively from the data without prior assumptions about the model structure, other than it is within the generic class of nonlinear differential-delay equations. The bottom-up modelling is developed using the TOPMODEL, whose structure is assumed a priori and is evaluated by global sensitivity analysis (GSA) in order to specify the most sensitive and important parameters. The subsequent exercises in calibration and validation, performed with Generalized Likelihood Uncertainty Estimation (GLUE), are carried out in the light of the GSA and DBM analyses. This allows for the pre-calibration of the the priors used for GLUE, in order to eliminate dynamical features of the TOPMODEL that have little effect on the model output and would be rejected at the structure identification phase of the DBM modelling analysis. In this way, the elements of meaningful subjectivity in the GLUE approach, which allow the modeler to interact in the modelling process by constraining the model to have a specific form prior to calibration, are combined with other more objective, data-based benchmarks for the final uncertainty estimation. GSA plays a major role in building a bridge between the hypothetico-deductive (bottom-up) and inductive (top-down) approaches and helps to improve the

Dynamic and accurate assessment of acetaminophen-induced hepatotoxicity by integrated photoacoustic imaging and mechanistic biomarkers in vivo.

Science.gov (United States)

Brillant, Nathalie; Elmasry, Mohamed; Burton, Neal C; Rodriguez, Josep Monne; Sharkey, Jack W; Fenwick, Stephen; Poptani, Harish; Kitteringham, Neil R; Goldring, Christopher E; Kipar, Anja; Park, B Kevin; Antoine, Daniel J

2017-10-01

The prediction and understanding of acetaminophen (APAP)-induced liver injury (APAP-ILI) and the response to therapeutic interventions is complex. This is due in part to sensitivity and specificity limitations of currently used assessment techniques. Here we sought to determine the utility of integrating translational non-invasive photoacoustic imaging of liver function with mechanistic circulating biomarkers of hepatotoxicity with histological assessment to facilitate the more accurate and precise characterization of APAP-ILI and the efficacy of therapeutic intervention. Perturbation of liver function and cellular viability was assessed in C57BL/6J male mice by Indocyanine green (ICG) clearance (Multispectral Optoacoustic Tomography (MSOT)) and by measurement of mechanistic (miR-122, HMGB1) and established (ALT, bilirubin) circulating biomarkers in response to the acetaminophen and its treatment with acetylcysteine (NAC) in vivo. We utilised a 60% partial hepatectomy model as a situation of defined hepatic functional mass loss to compared acetaminophen-induced changes to. Integration of these mechanistic markers correlated with histological features of APAP hepatotoxicity in a time-dependent manner. They accurately reflected the onset and recovery from hepatotoxicity compared to traditional biomarkers and also reported the efficacy of NAC with high sensitivity. ICG clearance kinetics correlated with histological scores for acute liver damage for APAP (i.e. 3h timepoint; r=0.90, P<0.0001) and elevations in both of the mechanistic biomarkers, miR-122 (e.g. 6h timepoint; r=0.70, P=0.005) and HMGB1 (e.g. 6h timepoint; r=0.56, P=0.04). For the first time we report the utility of this non-invasive longitudinal imaging approach to provide direct visualisation of the liver function coupled with mechanistic biomarkers, in the same animal, allowing the investigation of the toxicological and pharmacological aspects of APAP-ILI and hepatic regeneration. Copyright © 2017

Effects of Asphalt Mix Design Properties on Pavement Performance: A Mechanistic Approach

Directory of Open Access Journals (Sweden)

Ahmad M. Abu Abdo

2016-01-01

Full Text Available The main objective of this study was to investigate the effects of hot mix asphalt material properties on the performance of flexible pavements via mechanistic approach. 3D Move Analysis software was utilized to determine rutting and cracking distresses in an asphalt concrete (AC layer. Fourteen different Superpave mixes were evaluated by utilizing results of the Dynamic Modulus (|E⁎| Test and the Dynamic Shear Modulus (|G⁎| Test. Results showed that with the increase of binder content, the tendency of rutting in AC layer increased. However, with the increase of binder content, the cracking of AC layer lessened. Furthermore, when different binder grades were evaluated, results showed that with the increase of the upper binder grade number, rutting decreased, and with the increase of the lower binder grade number, rutting increased. Furthermore, analysis showed that with the increase of the lower binder grade number, higher percent of bottom up cracks would result. As a result of the analysis, binder grade should not be solely considered for cracking in AC layer; binder content and aggregate structure play a big role. Finally, results illustrated that the mechanistic approach is a better tool to determine the performance of asphalt pavement than commonly used methods.

Generative mechanistic explanation building in undergraduate molecular and cellular biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-09-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among scientists, we created and applied a theoretical framework to explore the strategies students use to construct explanations for 'novel' biological phenomena. Specifically, we explored how students navigated the multi-level nature of complex biological systems using generative mechanistic reasoning. Interviews were conducted with introductory and upper-division biology students at a large public university in the United States. Results of qualitative coding revealed key features of students' explanation building. Students used modular thinking to consider the functional subdivisions of the system, which they 'filled in' to varying degrees with mechanistic elements. They also hypothesised the involvement of mechanistic entities and instantiated abstract schema to adapt their explanations to unfamiliar biological contexts. Finally, we explored the flexible thinking that students used to hypothesise the impact of mutations on multi-leveled biological systems. Results revealed a number of ways that students drew mechanistic connections between molecules, functional modules (sets of molecules with an emergent function), cells, tissues, organisms and populations.

Development of Improved Mechanistic Deterioration Models for Flexible Pavements

DEFF Research Database (Denmark)

Ullidtz, Per; Ertman, Hans Larsen

1998-01-01

The paper describes a pilot study in Denmark with the main objective of developing improved mechanistic deterioration models for flexible pavements based on an accelerated full scale test on an instrumented pavement in the Danish Road Tessting Machine. The study was the first in "International...... Pavement Subgrade Performance Study" sponsored by the Federal Highway Administration (FHWA), USA. The paper describes in detail the data analysis and the resulting models for rutting, roughness, and a model for the plastic strain in the subgrade.The reader will get an understanding of the work needed...

Optical coherence tomography assessment of the mechanistic effects of rotational and orbital atherectomy in severely calcified coronary lesions.

Science.gov (United States)

Kini, Annapoorna S; Vengrenyuk, Yuliya; Pena, Jacobo; Motoyama, Sadako; Feig, Jonathan E; Meelu, Omar A; Rajamanickam, Anitha; Bhat, Arjun M; Panwar, Sadik; Baber, Usman; Sharma, Samin K

2015-11-15

This study sought to assess the mechanistic effect of rotational atherectomy (RA) and orbital atherectomy (OA) on heavily calcified coronary lesions and subsequent stent placement using optical coherence tomography (OCT). RA and OA are two main approaches to ablate coronary calcium. While small case reports have described the mechanistic effect of RA in calcified coronary lesions, there has been no imaging study to assess the effect of OA on coronary artery architecture and/or compare the effects of two atherectomy devices. This study analyzed 20 consecutive patients with OCT imaging performed after atherectomy and after stent implantation, RA (n = 10) and OA (n = 10). Postatherectomy OCT analysis identified tissue modification with deep dissections in around a third of lesions after RA and OA; however, post OA dissections ("lacunae") were significantly deeper (1.14 vs. 0.82 mm, P = 0.048). Post OA/RA lesions with dissections had significantly higher percentage of lipid rich plaques and smaller calcification arcs as compared to plaques without dissections. Stents after OA were associated with a significantly lower percent of stent strut malapposition than post RA stents (4.36 vs. 8.02%, P = 0.038). Although the incidence of dissections was comparable between RA and OA cases, OA resulted in deeper tissue modifications (lacunae) as shown by OCT imaging. The finding might provide an explanation for a better stent apposition after OA as compared to RA. Their impact on long-term outcome needs to be determined. © 2015 Wiley Periodicals, Inc.

"Ratio via Machina": Three Standards of Mechanistic Explanation in Sociology

Science.gov (United States)

Aviles, Natalie B.; Reed, Isaac Ariail

2017-01-01

Recently, sociologists have expended much effort in attempts to define social mechanisms. We intervene in these debates by proposing that sociologists in fact have a choice to make between three standards of what constitutes a good mechanistic explanation: substantial, formal, and metaphorical mechanistic explanation. All three standards are…

Toward mechanistic classification of enzyme functions.

Science.gov (United States)

Almonacid, Daniel E; Babbitt, Patricia C

2011-06-01

Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comparison of Two-Phase Pipe Flow in OpenFOAM with a Mechanistic Model

Science.gov (United States)

Shuard, Adrian M.; Mahmud, Hisham B.; King, Andrew J.

2016-03-01

Two-phase pipe flow is a common occurrence in many industrial applications such as power generation and oil and gas transportation. Accurate prediction of liquid holdup and pressure drop is of vast importance to ensure effective design and operation of fluid transport systems. In this paper, a Computational Fluid Dynamics (CFD) study of a two-phase flow of air and water is performed using OpenFOAM. The two-phase solver, interFoam is used to identify flow patterns and generate values of liquid holdup and pressure drop, which are compared to results obtained from a two-phase mechanistic model developed by Petalas and Aziz (2002). A total of 60 simulations have been performed at three separate pipe inclinations of 0°, +10° and -10° respectively. A three dimensional, 0.052m diameter pipe of 4m length is used with the Shear Stress Transport (SST) k - ɷ turbulence model to solve the turbulent mixtures of air and water. Results show that the flow pattern behaviour and numerical values of liquid holdup and pressure drop compare reasonably well to the mechanistic model.

Improving the International Agency for Research on Cancer's consideration of mechanistic evidence

International Nuclear Information System (INIS)

Goodman, Julie; Lynch, Heather

2017-01-01

Background: The International Agency for Research on Cancer (IARC) recently developed a framework for evaluating mechanistic evidence that includes a list of 10 key characteristics of carcinogens. This framework is useful for identifying and organizing large bodies of literature on carcinogenic mechanisms, but it lacks sufficient guidance for conducting evaluations that fully integrate mechanistic evidence into hazard assessments. Objectives: We summarize the framework, and suggest approaches to strengthen the evaluation of mechanistic evidence using this framework. Discussion: While the framework is useful for organizing mechanistic evidence, its lack of guidance for implementation limits its utility for understanding human carcinogenic potential. Specifically, it does not include explicit guidance for evaluating the biological significance of mechanistic endpoints, inter- and intra-individual variability, or study quality and relevance. It also does not explicitly address how mechanistic evidence should be integrated with other realms of evidence. Because mechanistic evidence is critical to understanding human cancer hazards, we recommend that IARC develop transparent and systematic guidelines for the use of this framework so that mechanistic evidence will be evaluated and integrated in a robust manner, and concurrently with other realms of evidence, to reach a final human cancer hazard conclusion. Conclusions: IARC does not currently provide a standardized approach to evaluating mechanistic evidence. Incorporating the recommendations discussed here will make IARC analyses of mechanistic evidence more transparent, and lead to assessments of cancer hazards that reflect the weight of the scientific evidence and allow for scientifically defensible decision-making. - Highlights: • IARC has a revised framework for evaluating literature on carcinogenic mechanisms. • The framework is based on 10 key characteristics of carcinogens. • IARC should develop transparent

Improving the International Agency for Research on Cancer's consideration of mechanistic evidence

Energy Technology Data Exchange (ETDEWEB)

Goodman, Julie, E-mail: jgoodman@gradientcorp.com; Lynch, Heather

2017-03-15

Background: The International Agency for Research on Cancer (IARC) recently developed a framework for evaluating mechanistic evidence that includes a list of 10 key characteristics of carcinogens. This framework is useful for identifying and organizing large bodies of literature on carcinogenic mechanisms, but it lacks sufficient guidance for conducting evaluations that fully integrate mechanistic evidence into hazard assessments. Objectives: We summarize the framework, and suggest approaches to strengthen the evaluation of mechanistic evidence using this framework. Discussion: While the framework is useful for organizing mechanistic evidence, its lack of guidance for implementation limits its utility for understanding human carcinogenic potential. Specifically, it does not include explicit guidance for evaluating the biological significance of mechanistic endpoints, inter- and intra-individual variability, or study quality and relevance. It also does not explicitly address how mechanistic evidence should be integrated with other realms of evidence. Because mechanistic evidence is critical to understanding human cancer hazards, we recommend that IARC develop transparent and systematic guidelines for the use of this framework so that mechanistic evidence will be evaluated and integrated in a robust manner, and concurrently with other realms of evidence, to reach a final human cancer hazard conclusion. Conclusions: IARC does not currently provide a standardized approach to evaluating mechanistic evidence. Incorporating the recommendations discussed here will make IARC analyses of mechanistic evidence more transparent, and lead to assessments of cancer hazards that reflect the weight of the scientific evidence and allow for scientifically defensible decision-making. - Highlights: • IARC has a revised framework for evaluating literature on carcinogenic mechanisms. • The framework is based on 10 key characteristics of carcinogens. • IARC should develop transparent

Predicting interactions from mechanistic information: Can omic data validate theories?

International Nuclear Information System (INIS)

Borgert, Christopher J.

2007-01-01

To address the most pressing and relevant issues for improving mixture risk assessment, researchers must first recognize that risk assessment is driven by both regulatory requirements and scientific research, and that regulatory concerns may expand beyond the purely scientific interests of researchers. Concepts of 'mode of action' and 'mechanism of action' are used in particular ways within the regulatory arena, depending on the specific assessment goals. The data requirements for delineating a mode of action and predicting interactive toxicity in mixtures are not well defined from a scientific standpoint due largely to inherent difficulties in testing certain underlying assumptions. Understanding the regulatory perspective on mechanistic concepts will be important for designing experiments that can be interpreted clearly and applied in risk assessments without undue reliance on extrapolation and assumption. In like fashion, regulators and risk assessors can be better equipped to apply mechanistic data if the concepts underlying mechanistic research and the limitations that must be placed on interpretation of mechanistic data are understood. This will be critically important for applying new technologies to risk assessment, such as functional genomics, proteomics, and metabolomics. It will be essential not only for risk assessors to become conversant with the language and concepts of mechanistic research, including new omic technologies, but also, for researchers to become more intimately familiar with the challenges and needs of risk assessment

Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

International Nuclear Information System (INIS)

Thomson, Ty M.; Sewer, Alain; Martin, Florian; Belcastro, Vincenzo; Frushour, Brian P.; Gebel, Stephan; Park, Jennifer; Schlage, Walter K.; Talikka, Marja; Vasilyev, Dmitry M.; Westra, Jurjen W.; Hoeng, Julia; Peitsch, Manuel C.

2013-01-01

Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. - Highlights: • The impact of biologically active substances is quantified at multiple levels. • The systems-level impact integrates the perturbations of individual networks. • The networks capture the relationships between

Crystal structure of the pestivirus envelope glycoprotein E(rns) and mechanistic analysis of its ribonuclease activity.

Science.gov (United States)

Krey, Thomas; Bontems, Francois; Vonrhein, Clemens; Vaney, Marie-Christine; Bricogne, Gerard; Rümenapf, Till; Rey, Félix A

2012-05-09

Pestiviruses, which belong to the Flaviviridae family of RNA viruses, are important agents of veterinary diseases causing substantial economical losses in animal farming worldwide. Pestivirus particles display three envelope glycoproteins at their surface: E(rns), E1, and E2. We report here the crystal structure of the catalytic domain of E(rns), the ribonucleolytic activity of which is believed to counteract the innate immunity of the host. The structure reveals a three-dimensional fold corresponding to T2 ribonucleases from plants and fungi. Cocrystallization experiments with mono- and oligonucleotides revealed the structural basis for substrate recognition at two binding sites previously identified for T2 RNases. A detailed analysis of poly-U cleavage products using (31)P-NMR and size exclusion chromatography, together with molecular docking studies, provides a comprehensive mechanistic picture of E(rns) activity on its substrates and reveals the presence of at least one additional nucleotide binding site. Copyright © 2012 Elsevier Ltd. All rights reserved.

Characteristics of genomic signatures derived using univariate methods and mechanistically anchored functional descriptors for predicting drug- and xenobiotic-induced nephrotoxicity.

Science.gov (United States)

Shi, Weiwei; Bugrim, Andrej; Nikolsky, Yuri; Nikolskya, Tatiana; Brennan, Richard J

2008-01-01

ABSTRACT The ideal toxicity biomarker is composed of the properties of prediction (is detected prior to traditional pathological signs of injury), accuracy (high sensitivity and specificity), and mechanistic relationships to the endpoint measured (biological relevance). Gene expression-based toxicity biomarkers ("signatures") have shown good predictive power and accuracy, but are difficult to interpret biologically. We have compared different statistical methods of feature selection with knowledge-based approaches, using GeneGo's database of canonical pathway maps, to generate gene sets for the classification of renal tubule toxicity. The gene set selection algorithms include four univariate analyses: t-statistics, fold-change, B-statistics, and RankProd, and their combination and overlap for the identification of differentially expressed probes. Enrichment analysis following the results of the four univariate analyses, Hotelling T-square test, and, finally out-of-bag selection, a variant of cross-validation, were used to identify canonical pathway maps-sets of genes coordinately involved in key biological processes-with classification power. Differentially expressed genes identified by the different statistical univariate analyses all generated reasonably performing classifiers of tubule toxicity. Maps identified by enrichment analysis or Hotelling T-square had lower classification power, but highlighted perturbed lipid homeostasis as a common discriminator of nephrotoxic treatments. The out-of-bag method yielded the best functionally integrated classifier. The map "ephrins signaling" performed comparably to a classifier derived using sparse linear programming, a machine learning algorithm, and represents a signaling network specifically involved in renal tubule development and integrity. Such functional descriptors of toxicity promise to better integrate predictive toxicogenomics with mechanistic analysis, facilitating the interpretation and risk assessment of

Mechanistic modelling of the drying behaviour of single pharmaceutical granules

DEFF Research Database (Denmark)

Thérèse F.C. Mortier, Séverine; Beer, Thomas De; Gernaey, Krist

2012-01-01

The trend to move towards continuous production processes in pharmaceutical applications enhances the necessity to develop mechanistic models to understand and control these processes. This work focuses on the drying behaviour of a single wet granule before tabletting, using a six...... phase (submodel 2), the water inside the granule evaporates. The second submodel contains an empirical power coefficient, b. A sensitivity analysis was performed to study the influence of parameters on the moisture content of single pharmaceutical granules, which clearly points towards the importance...

Mechanistic Modeling of Water Replenishment Rate of Zeer Refrigerator

Directory of Open Access Journals (Sweden)

B. N. Nwankwojike

2017-06-01

Full Text Available A model for predicting the water replenishment rate of zeer pot refrigerator was developed in this study using mechanistic modeling approach and evaluated at Obowo, Imo State, Nigeria using six fruits, tomatoes, guava, okra, banana, orange and avocado pear. The developed model confirmed zeer pot water replenishment rate as a function of ambient temperature, relative humidity, wind speed, thermal conductivity of the pot materials and sand, density of air and water vapor, permeability coefficient of clay and heat transfer coefficient of water into air, circumferential length, height of pot, geometrical profile of the pot, heat load of the food preserved, heat flow into the device and gradient at which the pot is placed above ground level. Compared to the conventional approach of water replenishment, performance analysis results revealed 44% to 58% water economy when the zeer pot’s water was replenished based on the model’s prediction; while there was no significant difference in the shelf-life of the fruits preserved with both replenishment methods. Application of the developed water replenishment model facilitates optimal water usage in this system, thereby reducing operational cost of zeer pot refrigerator.

Managing mechanistic and organic structure in health care organizations.

Science.gov (United States)

Olden, Peter C

2012-01-01

Managers at all levels in a health care organization must organize work to achieve the organization's mission and goals. This requires managers to decide the organization structure, which involves dividing the work among jobs and departments and then coordinating them all toward the common purpose. Organization structure, which is reflected in an organization chart, may range on a continuum from very mechanistic to very organic. Managers must decide how mechanistic versus how organic to make the entire organization and each of its departments. To do this, managers should carefully consider 5 factors for the organization and for each individual department: external environment, goals, work production, size, and culture. Some factors may push toward more mechanistic structure, whereas others may push in the opposite direction toward more organic structure. Practical advice can help managers at all levels design appropriate structure for their departments and organization.

Cognitive science as an interface between rational and mechanistic explanation.

Science.gov (United States)

Chater, Nick

2014-04-01

Cognitive science views thought as computation; and computation, by its very nature, can be understood in both rational and mechanistic terms. In rational terms, a computation solves some information processing problem (e.g., mapping sensory information into a description of the external world; parsing a sentence; selecting among a set of possible actions). In mechanistic terms, a computation corresponds to causal chain of events in a physical device (in engineering context, a silicon chip; in biological context, the nervous system). The discipline is thus at the interface between two very different styles of explanation--as the papers in the current special issue well illustrate, it explores the interplay of rational and mechanistic forces. Copyright © 2014 Cognitive Science Society, Inc.

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

Science.gov (United States)

Transtrum, Mark K; Qiu, Peng

2016-05-01

The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.

Linking spring phenology with mechanistic models of host movement to predict disease transmission risk

Science.gov (United States)

Merkle, Jerod A.; Cross, Paul C.; Scurlock, Brandon M.; Cole, Eric K.; Courtemanch, Alyson B.; Dewey, Sarah R.; Kauffman, Matthew J.

2018-01-01

Disease models typically focus on temporal dynamics of infection, while often neglecting environmental processes that determine host movement. In many systems, however, temporal disease dynamics may be slow compared to the scale at which environmental conditions alter host space-use and accelerate disease transmission.Using a mechanistic movement modelling approach, we made space-use predictions of a mobile host (elk [Cervus Canadensis] carrying the bacterial disease brucellosis) under environmental conditions that change daily and annually (e.g., plant phenology, snow depth), and we used these predictions to infer how spring phenology influences the risk of brucellosis transmission from elk (through aborted foetuses) to livestock in the Greater Yellowstone Ecosystem.Using data from 288 female elk monitored with GPS collars, we fit step selection functions (SSFs) during the spring abortion season and then implemented a master equation approach to translate SSFs into predictions of daily elk distribution for five plausible winter weather scenarios (from a heavy snow, to an extreme winter drought year). We predicted abortion events by combining elk distributions with empirical estimates of daily abortion rates, spatially varying elk seroprevelance and elk population counts.Our results reveal strong spatial variation in disease transmission risk at daily and annual scales that is strongly governed by variation in host movement in response to spring phenology. For example, in comparison with an average snow year, years with early snowmelt are predicted to have 64% of the abortions occurring on feedgrounds shift to occurring on mainly public lands, and to a lesser extent on private lands.Synthesis and applications. Linking mechanistic models of host movement with disease dynamics leads to a novel bridge between movement and disease ecology. Our analysis framework offers new avenues for predicting disease spread, while providing managers tools to proactively mitigate

Comparison of Two-Phase Pipe Flow in OpenFOAM with a Mechanistic Model

International Nuclear Information System (INIS)

Shuard, Adrian M; Mahmud, Hisham B; King, Andrew J

2016-01-01

Two-phase pipe flow is a common occurrence in many industrial applications such as power generation and oil and gas transportation. Accurate prediction of liquid holdup and pressure drop is of vast importance to ensure effective design and operation of fluid transport systems. In this paper, a Computational Fluid Dynamics (CFD) study of a two-phase flow of air and water is performed using OpenFOAM. The two-phase solver, interFoam is used to identify flow patterns and generate values of liquid holdup and pressure drop, which are compared to results obtained from a two-phase mechanistic model developed by Petalas and Aziz (2002). A total of 60 simulations have been performed at three separate pipe inclinations of 0°, +10° and -10° respectively. A three dimensional, 0.052m diameter pipe of 4m length is used with the Shear Stress Transport (SST) k - ω turbulence model to solve the turbulent mixtures of air and water. Results show that the flow pattern behaviour and numerical values of liquid holdup and pressure drop compare reasonably well to the mechanistic model. (paper)

Recognizing Mechanistic Reasoning in Student Scientific Inquiry: A Framework for Discourse Analysis Developed from Philosophy of Science

Science.gov (United States)

Russ, Rosemary S.; Scherr, Rachel E.; Hammer, David; Mikeska, Jamie

2008-01-01

Science education reform has long focused on assessing student inquiry, and there has been progress in developing tools specifically with respect to experimentation and argumentation. We suggest the need for attention to another aspect of inquiry, namely "mechanistic reasoning." Scientific inquiry focuses largely on understanding causal…

A comparative analysis of reactor lower head debris cooling models employed in the existing severe accident analysis codes

International Nuclear Information System (INIS)

Ahn, K.I.; Kim, D.H.; Kim, S.B.; Kim, H.D.

1998-08-01

MELCOR and MAAP4 are the representative severe accident analysis codes which have been developed for the integral analysis of the phenomenological reactor lower head corium cooling behavior. Main objectives of the present study is to identify merits and disadvantages of each relevant model through the comparative analysis of the lower plenum corium cooling models employed in these two codes. The final results will be utilized for the development of LILAC phenomenological models and for the continuous improvement of the existing MELCOR reactor lower head models, which are currently being performed at the KAERI. For these purposes, first, nine reference models are selected featuring the lower head corium behavior based on the existing experimental evidences and related models. Then main features of the selected models have been critically analyzed, and finally merits and disadvantages of each corresponding model have been summarized in the view point of realistic corium behavior and reasonable modeling. Being on these evidences, summarized and presented the potential improvements for developing more advanced models. The present study has been focused on the qualitative comparison of each model and so more detailed quantitative analysis is strongly required to obtain the final conclusions for their merits and disadvantages. In addition, in order to compensate the limitations of the current model, required further studies relating closely the detailed mechanistic models with the molten material movement and heat transfer based on phase-change in the porous medium, to the existing simple models. (author). 36 refs

Mechanistic modelling of gaseous fission product behaviour in UO2 fuel by Rtop code

International Nuclear Information System (INIS)

Kanukova, V.D.; Khoruzhii, O.V.; Kourtchatov, S.Y.; Likhanskii, V.V.; Matveew, L.V.

2002-01-01

The current status of a mechanistic modelling by the RTOP code of the fission product behaviour in polycrystalline UO 2 fuel is described. An outline of the code and implemented physical models is presented. The general approach to code validation is discussed. It is exemplified by the results of validation of the models of fuel oxidation and grain growth. The different models of intragranular and intergranular gas bubble behaviour have been tested and the sensitivity of the code in the framework of these models has been analysed. An analysis of available models of the resolution of grain face bubbles is also presented. The possibilities of the RTOP code are presented through the example of modelling behaviour of WWER fuel over the course of a comparative WWER-PWR experiment performed at Halden and by comparison with Yanagisawa experiments. (author)

Mechanistic Links Between PARP, NAD, and Brain Inflammation After TBI

Science.gov (United States)

2015-10-01

1 AWARD NUMBER: W81XWH-13-2-0091 TITLE: Mechanistic Links Between PARP, NAD , and Brain Inflammation After TBI PRINCIPAL INVESTIGATOR...COVERED 25 Sep 2014 - 24 Sep 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Mechanistic Links Between PARP, NAD , and Brain Inflammation After TBI 5b. GRANT...efficacy of veliparib and NAD as agents for suppressing inflammation and improving outcomes after traumatic brain injury. The animal models include

A dynamic and mechanistic model of PCB bioaccumulation in the European hake ( Merluccius merluccius)

Science.gov (United States)

Bodiguel, Xavier; Maury, Olivier; Mellon-Duval, Capucine; Roupsard, François; Le Guellec, Anne-Marie; Loizeau, Véronique

2009-08-01

Bioaccumulation is difficult to document because responses differ among chemical compounds, with environmental conditions, and physiological processes characteristic of each species. We use a mechanistic model, based on the Dynamic Energy Budget (DEB) theory, to take into account this complexity and study factors impacting accumulation of organic pollutants in fish through ontogeny. The bioaccumulation model proposed is a comprehensive approach that relates evolution of hake PCB contamination to physiological information about the fish, such as diet, metabolism, reserve and reproduction status. The species studied is the European hake ( Merluccius merluccius, L. 1758). The model is applied to study the total concentration and the lipid normalised concentration of 4 PCB congeners in male and female hakes from the Gulf of Lions (NW Mediterranean sea) and the Bay of Biscay (NE Atlantic ocean). Outputs of the model compare consistently to measurements over the life span of fish. Simulation results clearly demonstrate the relative effects of food contamination, growth and reproduction on the PCB bioaccumulation in hake. The same species living in different habitats and exposed to different PCB prey concentrations exhibit marked difference in the body accumulation of PCBs. At the adult stage, female hakes have a lower PCB concentration compared to males for a given length. We successfully simulated these sex-specific PCB concentrations by considering two mechanisms: a higher energy allocation to growth for females and a transfer of PCBs from the female to its eggs when allocating lipids from reserve to eggs. Finally, by its mechanistic description of physiological processes, the model is relevant for other species and sets the stage for a mechanistic understanding of toxicity and ecological effects of organic contaminants in marine organisms.

Detailed Mechanistic Studies on Palladium-Catalyzed Selective C-H Olefination with Aliphatic Alkenes: A Significant Influence of Proton Shuttling.

Science.gov (United States)

Deb, Arghya; Hazra, Avijit; Peng, Qian; Paton, Robert S; Maiti, Debabrata

2017-01-18

Directing group-assisted regioselective C-H olefination with electronically biased olefins is well studied. However, the incorporation of unactivated olefins has remained largely unsuccessful. A proper mechanistic understanding of olefination involving unactivated alkenes is therefore essential for enhancing their usage in future. In this Article, detailed experimental and computational mechanistic studies on palladium catalyzed C-H olefination with unactivated, aliphatic alkenes are described. The isolation of Pd(II) intermediates is shown to be effective for elucidating the elementary steps involved in catalytic olefination. Reaction rate and order determination, control experiments, isotopic labeling studies, and Hammett analysis have been used to understand the reaction mechanism. The results from these experimental studies implicate β-hydride elimination as the rate-determining step and that a mechanistic switch occurs between cationic and neutral pathway. Computational studies support this interpretation of the experimental evidence and are used to uncover the origins of selectivity.

Specialists without spirit: limitations of the mechanistic biomedical model.

Science.gov (United States)

Hewa, S; Hetherington, R W

1995-06-01

This paper examines the origin and the development of the mechanistic model of the human body and health in terms of Max Weber's theory of rationalization. It is argued that the development of Western scientific medicine is a part of the broad process of rationalization that began in sixteenth century Europe as a result of the Reformation. The development of the mechanistic view of the human body in Western medicine is consistent with the ideas of calculability, predictability, and control-the major tenets of the process of rationalization as described by Weber. In recent years, however, the limitations of the mechanistic model have been the topic of many discussions. George Engel, a leading advocate of general systems theory, is one of the leading proponents of a new medical model which includes the general quality of life, clean environment, and psychological, or spiritual stability of life. The paper concludes with consideration of the potential of Engel's proposed new model in the context of the current state of rationalization in modern industrialized society.

Why did Jacques Monod make the choice of mechanistic determinism?

Science.gov (United States)

Loison, Laurent

2015-06-01

The development of molecular biology placed in the foreground a mechanistic and deterministic conception of the functioning of macromolecules. In this article, I show that this conception was neither obvious, nor necessary. Taking Jacques Monod as a case study, I detail the way he gradually came loose from a statistical understanding of determinism to finally support a mechanistic understanding. The reasons of the choice made by Monod at the beginning of the 1950s can be understood only in the light of the general theoretical schema supported by the concept of mechanistic determinism. This schema articulates three fundamental notions for Monod, namely that of the rigidity of the sequence of the genetic program, that of the intrinsic stability of macromolecules (DNA and proteins), and that of the specificity of molecular interactions. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

Directory of Open Access Journals (Sweden)

Thibaud Rougier

Full Text Available Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa, an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5. We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local

Mechanistic Indicators of Childhood Asthma (MICA) Study

Science.gov (United States)

The Mechanistic Indicators of Childhood Asthma (MICA) Study has been designed to incorporate state-of-the-art technologies to examine the physiological and environmental factors that interact to increase the risk of asthmatic responses. MICA is primarily a clinically-bases obser...

Mechanistic multidimensional analysis of horizontal two-phase flows

International Nuclear Information System (INIS)

Tselishcheva, Elena A.; Antal, Steven P.; Podowski, Michael Z.

2010-01-01

The purpose of this paper is to discuss the results of analysis of two-phase flow in horizontal tubes. Two flow situations have been considered: gas/liquid flow in a long straight pipe, and similar flow conditions in a pipe with 90 deg. elbow. The theoretical approach utilizes a multifield modeling concept. A complete three-dimensional two-phase flow model has been implemented in a state-of-the-art computational multiphase fluid dynamics (CMFD) computer code, NPHASE. The overall model has been tested parametrically. Also, the results of NPHASE simulations have been compared against experimental data for a pipe with 90 deg. elbow.

Mechanistic rationalization of unusual sigmoidal kinetic profiles in the Machetti-De Sarlo cycloaddition reaction.

Science.gov (United States)

Mower, Matthew P; Blackmond, Donna G

2015-02-18

Unusual sigmoidal kinetic profiles in the Machetti-De Sarlo base-catalyzed 1,3-dipolar cycloaddition of acrylamide to N-methylnitroacetamide are rationalized by detailed in situ kinetic analysis. A dual role is uncovered in which a substrate acts as a precursor to catalyze its own reaction. Such kinetic studies provide a general protocol for distinguishing among different mechanistic origins of induction periods in complex organic reactions.

Comparative risk analysis

International Nuclear Information System (INIS)

Niehaus, F.

1988-01-01

In this paper, the risks of various energy systems are discussed considering severe accidents analysis, particularly the probabilistic safety analysis, and probabilistic safety criteria, and the applications of these criteria and analysis. The comparative risk analysis has demonstrated that the largest source of risk in every society is from daily small accidents. Nevertheless, we have to be more concerned about severe accidents. The comparative risk analysis of five different energy systems (coal, oil, gas, LWR and STEC (Solar)) for the public has shown that the main sources of risks are coal and oil. The latest comparative risk study of various energy has been conducted in the USA and has revealed that the number of victims from coal is 42 as many than victims from nuclear. A study for severe accidents from hydro-dams in United States has estimated the probability of dam failures at 1 in 10,000 years and the number of victims between 11,000 and 260,000. The average occupational risk from coal is one fatal accident in 1,000 workers/year. The probabilistic safety analysis is a method that can be used to assess nuclear energy risks, and to analyze the severe accidents, and to model all possible accident sequences and consequences. The 'Fault tree' analysis is used to know the probability of failure of the different systems at each point of accident sequences and to calculate the probability of risks. After calculating the probability of failure, the criteria for judging the numerical results have to be developed, that is the quantitative and qualitative goals. To achieve these goals, several systems have been devised by various countries members of AIEA. The probabilistic safety ana-lysis method has been developed by establishing a computer program permit-ting to know different categories of safety related information. 19 tabs. (author)

Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library.

Science.gov (United States)

Macdonald, Spencer S; Patel, Ankoor; Larmour, Veronica L C; Morgan-Lang, Connor; Hallam, Steven J; Mark, Brian L; Withers, Stephen G

2018-03-02

Glycoside phosphorylases have considerable potential as catalysts for the assembly of useful glycans for products ranging from functional foods and prebiotics to novel materials. However, the substrate diversity of currently identified phosphorylases is relatively small, limiting their practical applications. To address this limitation, we developed a high-throughput screening approach using the activated substrate 2,4-dinitrophenyl β-d-glucoside (DNPGlc) and inorganic phosphate for identifying glycoside phosphorylase activity and used it to screen a large insert metagenomic library. The initial screen, based on release of 2,4-dinitrophenyl from DNPGlc in the presence of phosphate, identified the gene bglP, encoding a retaining β-glycoside phosphorylase from the CAZy GH3 family. Kinetic and mechanistic analysis of the gene product, BglP, confirmed a double displacement ping-pong mechanism involving a covalent glycosyl-enzyme intermediate. X-ray crystallographic analysis provided insights into the phosphate-binding mode and identified a key glutamine residue in the active site important for substrate recognition. Substituting this glutamine for a serine swapped the substrate specificity from glucoside to N -acetylglucosaminide. In summary, we present a high-throughput screening approach for identifying β-glycoside phosphorylases, which was robust, simple to implement, and useful in identifying active clones within a metagenomics library. Implementation of this screen enabled discovery of a new glycoside phosphorylase class and has paved the way to devising simple ways in which enzyme specificity can be encoded and swapped, which has implications for biotechnological applications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Mechanistic phenotypes: an aggregative phenotyping strategy to identify disease mechanisms using GWAS data.

Directory of Open Access Journals (Sweden)

Jonathan D Mosley

Full Text Available A single mutation can alter cellular and global homeostatic mechanisms and give rise to multiple clinical diseases. We hypothesized that these disease mechanisms could be identified using low minor allele frequency (MAF<0.1 non-synonymous SNPs (nsSNPs associated with "mechanistic phenotypes", comprised of collections of related diagnoses. We studied two mechanistic phenotypes: (1 thrombosis, evaluated in a population of 1,655 African Americans; and (2 four groupings of cancer diagnoses, evaluated in 3,009 white European Americans. We tested associations between nsSNPs represented on GWAS platforms and mechanistic phenotypes ascertained from electronic medical records (EMRs, and sought enrichment in functional ontologies across the top-ranked associations. We used a two-step analytic approach whereby nsSNPs were first sorted by the strength of their association with a phenotype. We tested associations using two reverse genetic models and standard additive and recessive models. In the second step, we employed a hypothesis-free ontological enrichment analysis using the sorted nsSNPs to identify functional mechanisms underlying the diagnoses comprising the mechanistic phenotypes. The thrombosis phenotype was solely associated with ontologies related to blood coagulation (Fisher's p = 0.0001, FDR p = 0.03, driven by the F5, P2RY12 and F2RL2 genes. For the cancer phenotypes, the reverse genetics models were enriched in DNA repair functions (p = 2×10-5, FDR p = 0.03 (POLG/FANCI, SLX4/FANCP, XRCC1, BRCA1, FANCA, CHD1L while the additive model showed enrichment related to chromatid segregation (p = 4×10-6, FDR p = 0.005 (KIF25, PINX1. We were able to replicate nsSNP associations for POLG/FANCI, BRCA1, FANCA and CHD1L in independent data sets. Mechanism-oriented phenotyping using collections of EMR-derived diagnoses can elucidate fundamental disease mechanisms.

The E. coli pET expression system revisited-mechanistic correlation between glucose and lactose uptake.

Science.gov (United States)

Wurm, David Johannes; Veiter, Lukas; Ulonska, Sophia; Eggenreich, Britta; Herwig, Christoph; Spadiut, Oliver

2016-10-01

Therapeutic monoclonal antibodies are mainly produced in mammalian cells to date. However, unglycosylated antibody fragments can also be produced in the bacterium Escherichia coli which brings several advantages, like growth on cheap media and high productivity. One of the most popular E. coli strains for recombinant protein production is E. coli BL21(DE3) which is usually used in combination with the pET expression system. However, it is well known that induction by isopropyl β-D-1-thiogalactopyranoside (IPTG) stresses the cells and can lead to the formation of insoluble inclusion bodies. In this study, we revisited the pET expression system for the production of a novel antibody single-chain variable fragment (scFv) with the goal of maximizing the amount of soluble product. Thus, we (1) investigated whether lactose favors the recombinant production of soluble scFv compared to IPTG, (2) investigated whether the formation of soluble product can be influenced by the specific glucose uptake rate (q s,glu) during lactose induction, and (3) determined the mechanistic correlation between the specific lactose uptake rate (q s,lac) and q s,glu. We found that lactose induction gave a much greater amount of soluble scFv compared to IPTG, even when the growth rate was increased. Furthermore, we showed that the production of soluble protein could be tuned by varying q s,glu during lactose induction. Finally, we established a simple model describing the mechanistic correlation between q s,lac and q s,glu allowing tailored feeding and prevention of sugar accumulation. We believe that this mechanistic model might serve as platform knowledge for E. coli.

Mechanistic aspects of ionic reactions in flames

DEFF Research Database (Denmark)

Egsgaard, H.; Carlsen, L.

1993-01-01

Some fundamentals of the ion chemistry of flames are summarized. Mechanistic aspects of ionic reactions in flames have been studied using a VG PlasmaQuad, the ICP-system being substituted by a simple quartz burner. Simple hydrocarbon flames as well as sulfur-containing flames have been investigated...

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.

Science.gov (United States)

Smith, Gregory R; Birtwistle, Marc R

2016-01-01

A main application for mRNA sequencing (mRNAseq) is determining lists of differentially-expressed genes (DEGs) between two or more conditions. Several software packages exist to produce DEGs from mRNAseq data, but they typically yield different DEGs, sometimes markedly so. The underlying probability model used to describe mRNAseq data is central to deriving DEGs, and not surprisingly most softwares use different models and assumptions to analyze mRNAseq data. Here, we propose a mechanistic justification to model mRNAseq as a binomial process, with data from technical replicates given by a binomial distribution, and data from biological replicates well-described by a beta-binomial distribution. We demonstrate good agreement of this model with two large datasets. We show that an emergent feature of the beta-binomial distribution, given parameter regimes typical for mRNAseq experiments, is the well-known quadratic polynomial scaling of variance with the mean. The so-called dispersion parameter controls this scaling, and our analysis suggests that the dispersion parameter is a continually decreasing function of the mean, as opposed to current approaches that impose an asymptotic value to the dispersion parameter at moderate mean read counts. We show how this leads to current approaches overestimating variance for moderately to highly expressed genes, which inflates false negative rates. Describing mRNAseq data with a beta-binomial distribution thus may be preferred since its parameters are relatable to the mechanistic underpinnings of the technique and may improve the consistency of DEG analysis across softwares, particularly for moderately to highly expressed genes.

Applicability of one-dimensional mechanistic post-dryout prediction model

International Nuclear Information System (INIS)

Jeong, Hae Yong; No Hee Cheon

1996-01-01

Through the analysis of many experimental post-dryout data, it is shown that the most probable flow regime near dryout or quench front is not annular flow but churn-turbulent flow when the mass flux is low. A correlation describing the initial droplet size just after the CHF position at low mass flux is low. A correlation describing the initial droplet size just after the CHF position at low mass flux is suggested through regression analysis. In the post-dryout region at low pressure and low flow, it is found that the suggested one-dimensional mechanistic model is not applicable when the vapor superficial velocity is very low, i. e., when the flow is bubbly or slug flow regime. This is explained by the change of main entrainment mechanism with the change of flow regime. Therefore, the suggested correlation is valid only in the churn-turbulent flow regime (j * g = 0.5 ∼ 4.5)

Thermal tides and studies to tune the mechanistic tidal model using UARS observations

Directory of Open Access Journals (Sweden)

V. A. Yudin

1997-09-01

Full Text Available Monthly simulations of the thermal diurnal and semidiurnal tides are compared to High-Resolution Doppler Imager (HRDI and Wind Imaging Interferometer (WINDII wind and temperature measurements on the Upper-Atmosphere Research Satellite (UARS. There is encouraging agreement between the observations and the linear global mechanistic tidal model results both for the diurnal and semidiurnal components in the equatorial and mid-latitude regions. This gives us the confidence to outline the first steps of an assimilative analysis/interpretation for tides, dissipation, and mean flow using a combination of model results and the global measurements from HRDI and WINDII. The sensitivity of the proposed technique to the initial guess employed to obtain a best fit to the data by tuning model parameters is discussed for the January and March 1993 cases, when the WINDII day and night measurements of the meridional winds between 90 and 110 km are used along with the daytime HRDI measurements. Several examples for the derivation of the tidal variables and decomposition of the measured winds into tidal and mean flow components using this approach are compared with previous tidal estimates and modeling results for the migrating tides. The seasonal cycle of the derived diurnal tidal amplitudes are discussed and compared with radar observation between 80 and 100 km and 40°S and 40°N.

Thermal tides and studies to tune the mechanistic tidal model using UARS observations

Directory of Open Access Journals (Sweden)

V. A. Yudin

Full Text Available Monthly simulations of the thermal diurnal and semidiurnal tides are compared to High-Resolution Doppler Imager (HRDI and Wind Imaging Interferometer (WINDII wind and temperature measurements on the Upper-Atmosphere Research Satellite (UARS. There is encouraging agreement between the observations and the linear global mechanistic tidal model results both for the diurnal and semidiurnal components in the equatorial and mid-latitude regions. This gives us the confidence to outline the first steps of an assimilative analysis/interpretation for tides, dissipation, and mean flow using a combination of model results and the global measurements from HRDI and WINDII. The sensitivity of the proposed technique to the initial guess employed to obtain a best fit to the data by tuning model parameters is discussed for the January and March 1993 cases, when the WINDII day and night measurements of the meridional winds between 90 and 110 km are used along with the daytime HRDI measurements. Several examples for the derivation of the tidal variables and decomposition of the measured winds into tidal and mean flow components using this approach are compared with previous tidal estimates and modeling results for the migrating tides. The seasonal cycle of the derived diurnal tidal amplitudes are discussed and compared with radar observation between 80 and 100 km and 40^°S and 40^°N.

Mechanistic Fermentation Models for Process Design, Monitoring, and Control

DEFF Research Database (Denmark)

Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla

2017-01-01

Mechanistic models require a significant investment of time and resources, but their application to multiple stages of fermentation process development and operation can make this investment highly valuable. This Opinion article discusses how an established fermentation model may be adapted...... for application to different stages of fermentation process development: planning, process design, monitoring, and control. Although a longer development time is required for such modeling methods in comparison to purely data-based model techniques, the wide range of applications makes them a highly valuable tool...... for fermentation research and development. In addition, in a research environment, where collaboration is important, developing mechanistic models provides a platform for knowledge sharing and consolidation of existing process understanding....

Incorporation of lysosomal sequestration in the mechanistic model for prediction of tissue distribution of basic drugs.

Science.gov (United States)

Assmus, Frauke; Houston, J Brian; Galetin, Aleksandra

2017-11-15

The prediction of tissue-to-plasma water partition coefficients (Kpu) from in vitro and in silico data using the tissue-composition based model (Rodgers & Rowland, J Pharm Sci. 2005, 94(6):1237-48.) is well established. However, distribution of basic drugs, in particular into lysosome-rich lung tissue, tends to be under-predicted by this approach. The aim of this study was to develop an extended mechanistic model for the prediction of Kpu which accounts for lysosomal sequestration and the contribution of different cell types in the tissue of interest. The extended model is based on compound-specific physicochemical properties and tissue composition data to describe drug ionization, distribution into tissue water and drug binding to neutral lipids, neutral phospholipids and acidic phospholipids in tissues, including lysosomes. Physiological data on the types of cells contributing to lung, kidney and liver, their lysosomal content and lysosomal pH were collated from the literature. The predictive power of the extended mechanistic model was evaluated using a dataset of 28 basic drugs (pK a ≥7.8, 17 β-blockers, 11 structurally diverse drugs) for which experimentally determined Kpu data in rat tissue have been reported. Accounting for the lysosomal sequestration in the extended mechanistic model improved the accuracy of Kpu predictions in lung compared to the original Rodgers model (56% drugs within 2-fold or 88% within 3-fold of observed values). Reduction in the extent of Kpu under-prediction was also evident in liver and kidney. However, consideration of lysosomal sequestration increased the occurrence of over-predictions, yielding overall comparable model performances for kidney and liver, with 68% and 54% of Kpu values within 2-fold error, respectively. High lysosomal concentration ratios relative to cytosol (>1000-fold) were predicted for the drugs investigated; the extent differed depending on the lysosomal pH and concentration of acidic phospholipids among

Comparative investigation on cation-cation (Al-Sn) and cation-anion (Al-F) co-doping in RF sputtered ZnO thin films: Mechanistic insight

Energy Technology Data Exchange (ETDEWEB)

Mallick, Arindam; Basak, Durga, E-mail: sspdb@iacs.res.in

2017-07-15

Highlights: • Comparative study on Al, Al-Sn and Al-F doped ZnO films has been carried out. • High transparent Al-F co-doped film shows three times enhanced carrier density. • Al-F co-doped film shows larger carrier relaxation time. • Al-Sn co-doped films shows carrier transport dominated by impurity scattering. • Al-F co-doped ZnO film can be applied as transparent electrode. - Abstract: Herein, we report a comparative mechanistic study on cation-cation (Al-Sn) and cation-anion (Al-F) co-doped nanocrystalline ZnO thin films grown on glass substrate by RF sputtering technique. Through detailed analyses of crystal structure, surface morphology, microstructure, UV-VIS-NIR transmission-reflection and electrical transport property, the inherent characteristics of the co-doped films were revealed and compared. All the nanocrystalline films retain the hexagonal wurtzite structure of ZnO and show transparency above 90% in the visible and NIR region. As opposed to expectation, Al-Sn (ATZO) co-doped film show no enhanced carrier concentration consistent with the probable formation of SnO{sub 2} clusters supported by the X-ray photoelectron spectroscopy study. Most interestingly, it has been found that Al-F (AFZO) co-doped film shows three times enhanced carrier concentration as compared to Al doped and Al-Sn co-doped films attaining a value of ∼9 × 10{sup 20} cm{sup −3} due to the respective cation and anion substitution. The carrier relaxation time increases in AFZO while it decreases significantly for ATZO film consistent with the concurrence of the impurity scattering in the latter.

Descriptive and mechanistic models of crop–weed competition

NARCIS (Netherlands)

Bastiaans, L.; Storkey, J.

2017-01-01

Crop-weed competitive relations are an important element of agroecosystems. Quantifying and understanding them helps to design appropriate weed management at operational, tactical and strategic level. This chapter presents and discusses simple descriptive and more mechanistic models for crop-weed

A mechanistic Eulerian-Lagrangian model for dispersed flow film boiling

International Nuclear Information System (INIS)

Andreani, M.; Yadigaroglu, G.

1991-01-01

In this paper a new mechanistic model of heat transfer in the dispersed flow regime is presented. The usual assumptions that render most of the available models unsuitable for the analysis of the reflooding phase of the LOCA are discussed, and a two-dimensional time-independent numerical model is developed. The gas temperature field is solved in a fixed-grid (Eulerian) mesh, with the droplets behaving as mass and energy sources. The histories of a large number of computational droplets are followed in a Lagrangian frame, considering evaporation, break-up and interactions with the vapor and with the wall. comparisons of calculated wall and vapor temperatures with experimental data are shown for two reflooding tests

Precision and accuracy of mechanistic-empirical pavement design

CSIR Research Space (South Africa)

Theyse, HL

2006-09-01

Full Text Available are discussed in general. The effects of variability and error on the design accuracy and design risk are lastly illustrated at the hand of a simple mechanistic-empirical design problem, showing that the engineering models alone determine the accuracy...

Mechanistic Models for Process Development and Optimization of Fed-batch Fermentation Systems

DEFF Research Database (Denmark)

Mears, Lisa; Stocks, Stuart M.; Albæk, Mads O.

2016-01-01

This work discusses the application of mechanistic models to pilot scale filamentous fungal fermentation systems operated at Novozymes A/S. For on-line applications, a state estimator model is developed based on a stoichiometric balance in order to predict the biomass and product concentration....... This is based on on-line gas measurements and ammonia addition flow rate measurements. Additionally, a mechanistic model is applied offline as a tool for batch planning, based on definition of the process back pressure, aeration rate and stirrer speed. This allows the batch starting fill to be planned, taking...... into account the oxygen transfer conditions, as well as the evaporation rates of the system. Mechanistic models are valuable tools which are applicable for both process development and optimization. The state estimator described will be a valuable tool for future work as part of control strategy development...

Requirements on mechanistic NPP models used in CSS for diagnostics and predictions

International Nuclear Information System (INIS)

Juslin, K.

1996-01-01

Mechanistic models have for several years with good experience been used for operators' support in electric power dispatching centres. Some models of limited scope have already been in use at nuclear power plants. It is considered that also advanced mechanistic models in combination with present computer technology with preference could be used in Computerized Support Systems (CSS) for the assistance of Nuclear Power Plant (NPP) operators. Requirements with respect to accuracy, validity range, speed flexibility and level of detail on the models used for such purposes are discussed. Quality Assurance, Verification and Validation efforts are considered. A long term commitment in the field of mechanistic modelling and real time simulation is considered as the key to successful implementations. The Advanced PROcess Simulation (APROS) code system and simulation environment developed at the Technical Research Centre of Finland (VTT) is intended also for CSS applications in NPP control rooms. (author). 4 refs

RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.

Science.gov (United States)

Auerbach, Scott S; Phadke, Dhiral P; Mav, Deepak; Holmgren, Stephanie; Gao, Yuan; Xie, Bin; Shin, Joo Heon; Shah, Ruchir R; Merrick, B Alex; Tice, Raymond R

2015-07-01

Formalin-fixed, paraffin-embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic-based biomarker discovery. We present here a comparison of results from a whole transcriptome RNA-Seq analysis of RNA extracted from fresh frozen and FFPE livers. The samples were derived from rats exposed to aflatoxin B1 (AFB1 ) and a corresponding set of control animals. Principal components analysis indicated that samples were separated in the two groups representing presence or absence of chemical exposure, both in fresh frozen and FFPE sample types. Sixty-five percent of the differentially expressed transcripts (AFB1 vs. controls) in fresh frozen samples were also differentially expressed in FFPE samples (overlap significance: P < 0.0001). Genomic signature and gene set analysis of AFB1 differentially expressed transcript lists indicated highly similar results between fresh frozen and FFPE at the level of chemogenomic signatures (i.e., single chemical/dose/duration elicited transcriptomic signatures), mechanistic and pathology signatures, biological processes, canonical pathways and transcription factor networks. Overall, our results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples. These results indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature-based biomarker discovery and mechanistic characterization of toxicity. Copyright © 2014 John Wiley & Sons, Ltd.

Mechanistic model for microbial growth on hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Mallee, F M; Blanch, H W

1977-12-01

Based on available information describing the transport and consumption of insoluble alkanes, a mechanistic model is proposed for microbial growth on hydrocarbons. The model describes the atypical growth kinetics observed, and has implications in the design of large scale equipment for single cell protein (SCP) manufacture from hydrocarbons. The model presents a framework for comparison of the previously published experimental kinetic data.

Mechanistic modelling of genetic and epigenetic events in radiation carcinogenesis

International Nuclear Information System (INIS)

Andreev, S. G.; Eidelman, Y. A.; Salnikov, I. V.; Khvostunov, I. K.

2006-01-01

Methodological problems arise on the way of radiation carcinogenesis modelling with the incorporation of radiobiological and cancer biology mechanistic data. The results of biophysical modelling of different endpoints [DNA DSB induction, repair, chromosome aberrations (CA) and cell proliferation] are presented and applied to the analysis of RBE-LET relationships for radiation-induced neoplastic transformation (RINT) of C3H/10T1/2 cells in culture. Predicted values for some endpoints correlate well with the data. It is concluded that slowly repaired DSB clusters, as well as some kind of CA, may be initiating events for RINT. As an alternative interpretation, it is possible that DNA damage can induce RINT indirectly via epigenetic process. A hypothetical epigenetic pathway for RINT is discussed. (authors)

A comparative kinetic and mechanistic study between tetrahydrozoline and naphazoline toward photogenerated reactive oxygen species.

Science.gov (United States)

Criado, Susana; García, Norman A

2010-01-01

Kinetic and mechanistic aspects of the vitamin B2 (riboflavin [Rf])-sensitized photo-oxidation of the imidazoline derivates (IDs) naphazoline (NPZ) and tetrahydrozoline (THZ) were investigated in aqueous solution. The process appears as important on biomedical grounds, considering that the vitamin is endogenously present in humans, and IDs are active components of ocular medicaments of topical application. Under aerobic visible light irradiation, a complex picture of competitive interactions between sensitizer, substrates and dissolved oxygen takes place: the singlet and triplet ((3)Rf*) excited states of Rf are quenched by the IDs: with IDs concentrations ca. 5.0 mM and 0.02 mM Rf, (3)Rf* is quenched by IDs, in a competitive fashion with dissolved ground state oxygen. Additionally, the reactive oxygen species: O(2)((1)Delta(g)), O(2)(*-), HO(*) and H(2)O(2), generated from (3)Rf* and Rf(*-), were detected with the employment of time-resolved methods or specific scavengers. Oxygen uptake experiments indicate that, for NPZ, only H(2)O(2) was involved in the photo-oxidation. In the case of THZ, O(2)(*-), HO(*) and H(2)O(2) were detected, whereas only HO(*) was unambiguously identified as THZ oxidative agents. Upon direct UV light irradiation NPZ and THZ generate O(2)((1)Delta(g)), with quantum yields of 0.2 (literature value, employed as a reference) and 0.08, respectively, in acetonitrile.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

Mechanistic model for void distribution in flashing flow

International Nuclear Information System (INIS)

Riznic, J.; Ishii, M.; Afgan, N.

1987-01-01

A problem of discharging of an initially subcooled liquid from a high pressure condition into a low pressure environment is quite important in several industrial systems such as nuclear reactors and chemical reactors. A new model for the flashing process is proposed here based on the wall nucleation theory, bubble growth model and drift-flux bubble transport model. In order to calculate the bubble number density, the bubble number transport equation with a distributed source from the wall nucleation sites is used. The model predictions in terms of the void fraction are compared to Moby Dick and BNL experimental data. It shows that satisfactory agreements could be obtained from the present model without any floating parameter to be adjusted with data. This result indicates that, at least for the experimental conditions considered here, the mechanistic prediction of the flashing phenomenon is possible based on the present wall nucleation based model. 43 refs., 4 figs

The mechanistic bases of the power-time relationship

DEFF Research Database (Denmark)

Vanhatalo, Anni; Black, Matthew I; DiMenna, Fred J

2016-01-01

.025) and inversely correlated with muscle type IIx fibre proportion (r = -0.76, P = 0.01). There was no relationship between W' (19.4 ± 6.3 kJ) and muscle fibre type. These data indicate a mechanistic link between the bioenergetic characteristics of different muscle fibre types and the power-duration relationship...

Navigating the complexities of qualitative comparative analysis: case numbers, necessity relations, and model ambiguities.

Science.gov (United States)

Thiem, Alrik

2014-12-01

In recent years, the method of Qualitative Comparative Analysis (QCA) has been enjoying increasing levels of popularity in evaluation and directly neighboring fields. Its holistic approach to causal data analysis resonates with researchers whose theories posit complex conjunctions of conditions and events. However, due to QCA's relative immaturity, some of its technicalities and objectives have not yet been well understood. In this article, I seek to raise awareness of six pitfalls of employing QCA with regard to the following three central aspects: case numbers, necessity relations, and model ambiguities. Most importantly, I argue that case numbers are irrelevant to the methodological choice of QCA or any of its variants, that necessity is not as simple a concept as it has been suggested by many methodologists, and that doubt must be cast on the determinacy of virtually all results presented in past QCA research. By means of empirical examples from published articles, I explain the background of these pitfalls and introduce appropriate procedures, partly with reference to current software, that help avoid them. QCA carries great potential for scholars in evaluation and directly neighboring areas interested in the analysis of complex dependencies in configurational data. If users beware of the pitfalls introduced in this article, and if they avoid mechanistic adherence to doubtful "standards of good practice" at this stage of development, then research with QCA will gain in quality, as a result of which a more solid foundation for cumulative knowledge generation and well-informed policy decisions will also be created. © The Author(s) 2014.

Mechanistic and kinetic insights into the thermally induced rearrangement of alpha-pinene.

Science.gov (United States)

Stolle, Achim; Ondruschka, Bernd; Findeisen, Matthias

2008-11-07

The thermal rearrangement of alpha-pinene (1) is interesting from mechanistic as well as kinetic point of view. Carrier gas pyrolyses with 1 and its acyclic isomers ocimene (2) and alloocimene (3) were performed to investigate the thermal network of these hydrocarbons. Kinetic analysis of the major reaction steps allows for a deeper insight in the reaction mechanism. Thus it was possible to explain the racemization of 1, the formation of racemic limonene (4), and the absence of the primary pyrolysis product 2 in the reaction mixture resulting from thermal rearrangement of 1. Results supported the conclusion that the reactions starting with 1 involve biradical transition states.

Mechanistic studies of carbon monoxide reduction

Energy Technology Data Exchange (ETDEWEB)

Geoffroy, G.L.

1990-06-12

The progress made during the current grant period (1 January 1988--1 April 1990) in three different areas of research is summarized. The research areas are: (1) oxidatively-induced double carbonylation reactions to form {alpha}-ketoacyl complexes and studies of the reactivity of the resulting compounds, (2) mechanistic studies of the carbonylation of nitroaromatics to form isocyanates, carbamates, and ureas, and (3) studies of the formation and reactivity of unusual metallacycles and alkylidene ligands supported on binuclear iron carbonyl fragments. 18 refs., 5 figs., 1 tab.

Advanced reach tool (ART) : Development of the mechanistic model

NARCIS (Netherlands)

Fransman, W.; Tongeren, M. van; Cherrie, J.W.; Tischer, M.; Schneider, T.; Schinkel, J.; Kromhout, H.; Warren, N.; Goede, H.; Tielemans, E.

2011-01-01

This paper describes the development of the mechanistic model within a collaborative project, referred to as the Advanced REACH Tool (ART) project, to develop a tool to model inhalation exposure for workers sharing similar operational conditions across different industries and locations in Europe.

The physicochemical process of bacterial attachment to abiotic surfaces: Challenges for mechanistic studies, predictability and the development of control strategies.

Science.gov (United States)

Wang, Yi; Lee, Sui Mae; Dykes, Gary

2015-01-01

Bacterial attachment to abiotic surfaces can be explained as a physicochemical process. Mechanisms of the process have been widely studied but are not yet well understood due to their complexity. Physicochemical processes can be influenced by various interactions and factors in attachment systems, including, but not limited to, hydrophobic interactions, electrostatic interactions and substratum surface roughness. Mechanistic models and control strategies for bacterial attachment to abiotic surfaces have been established based on the current understanding of the attachment process and the interactions involved. Due to a lack of process control and standardization in the methodologies used to study the mechanisms of bacterial attachment, however, various challenges are apparent in the development of models and control strategies. In this review, the physicochemical mechanisms, interactions and factors affecting the process of bacterial attachment to abiotic surfaces are described. Mechanistic models established based on these parameters are discussed in terms of their limitations. Currently employed methods to study these parameters and bacterial attachment are critically compared. The roles of these parameters in the development of control strategies for bacterial attachment are reviewed, and the challenges that arise in developing mechanistic models and control strategies are assessed.

Application of mechanistic empirical approach to predict rutting of superpave mixtures in Iraq

Directory of Open Access Journals (Sweden)

Qasim Zaynab

2018-01-01

Full Text Available In Iraq rutting is considered as a real distress in flexible pavements as a result of high summer temperature, and increased axle loads. This distress majorly affects asphalt pavement performance, lessens the pavement useful service life and makes serious hazards for highway users. Performance of HMA mixtures against rutting using Mechanistic- Empirical approach is predicted by considering Wheel-Tracking test and employing the Superpave mix design requirements. Roller Wheel Compactor has been locally manufactured to prepare slab specimens. In view of study laboratory outcomes that are judged to be simulative of field loading conditions, models are developed for predicting permanent strain of compacted samples of local asphalt concrete mixtures after considering the stress level, properties of local material and environmental impacts variables. All in all, laboratory results were produced utilizing statistical analysis with the aid of SPSS software. Permanent strain models for asphalt concrete mixtures were developed as a function of: number of passes, temperature, asphalt content, viscosity, air voids and additive content. Mechanistic Empirical design approach through the MnPAVE software was applied to characterize rutting in HMA and to predict allowable number of loading repetitions of mixtures as a function of expected traffic loads, material properties, and environmental temperature.

Electrochemical processes and mechanistic aspects of field-effect sensors for biomolecules

Science.gov (United States)

Huang, Weiguo; Diallo, Abdou Karim; Dailey, Jennifer L.; Besar, Kalpana

2017-01-01

Electronic biosensing is a leading technology for determining concentrations of biomolecules. In some cases, the presence of an analyte molecule induces a measured change in current flow, while in other cases, a new potential difference is established. In the particular case of a field effect biosensor, the potential difference is monitored as a change in conductance elsewhere in the device, such as across a film of an underlying semiconductor. Often, the mechanisms that lead to these responses are not specifically determined. Because improved understanding of these mechanisms will lead to improved performance, it is important to highlight those studies where various mechanistic possibilities are investigated. This review explores a range of possible mechanistic contributions to field-effect biosensor signals. First, we define the field-effect biosensor and the chemical interactions that lead to the field effect, followed by a section on theoretical and mechanistic background. We then discuss materials used in field-effect biosensors and approaches to improving signals from field-effect biosensors. We specifically cover the biomolecule interactions that produce local electric fields, structures and processes at interfaces between bioanalyte solutions and electronic materials, semiconductors used in biochemical sensors, dielectric layers used in top-gated sensors, and mechanisms for converting the surface voltage change to higher signal/noise outputs in circuits. PMID:29238595

Comparative proteomics analysis of proteins expressed in the I-1 and I-2 internodes of strawberry stolons

Directory of Open Access Journals (Sweden)

Lai Wenguo

2011-05-01

Full Text Available Abstract Background Strawberries (Fragaria ananassa reproduce asexually through stolons, which have strong tendencies to form adventitious roots at their second node. Understanding how the development of the proximal (I-1 and distal (I-2 internodes of stolons differ should facilitate nursery cultivation of strawberries. Results Herein, we compared the proteomic profiles of the strawberry stolon I-1 and I-2 internodes. Proteins extracted from the internodes were separated by two-dimensional gel electrophoresis, and 164 I-1 protein spots and 200 I-2 protein spots were examined further. Using mass spectrometry and database searches, 38 I-1 and 52 I-2 proteins were identified and categorized (8 and 10 groups, respectively according to their cellular compartmentalization and functionality. Many of the identified proteins are enzymes necessary for carbohydrate metabolism and photosynthesis. Furthermore, identification of proteins that interact revealed that many of the I-2 proteins form a dynamic network during development. Finally, given our results, we present a mechanistic scheme for adventitious root formation of new clonal plants at the second node. Conclusions Comparative proteomic analysis of I-1 and I-2 proteins revealed that the ubiquitin-proteasome pathway and sugar-hormone pathways might be important during adventitious root formation at the second node of new clonal plants.

Mechanistic applicability domain classification of a local lymph node assay dataset for skin sensitization.

Science.gov (United States)

Roberts, David W; Patlewicz, Grace; Kern, Petra S; Gerberick, Frank; Kimber, Ian; Dearman, Rebecca J; Ryan, Cindy A; Basketter, David A; Aptula, Aynur O

2007-07-01

The goal of eliminating animal testing in the predictive identification of chemicals with the intrinsic ability to cause skin sensitization is an important target, the attainment of which has recently been brought into even sharper relief by the EU Cosmetics Directive and the requirements of the REACH legislation. Development of alternative methods requires that the chemicals used to evaluate and validate novel approaches comprise not only confirmed skin sensitizers and non-sensitizers but also substances that span the full chemical mechanistic spectrum associated with skin sensitization. To this end, a recently published database of more than 200 chemicals tested in the mouse local lymph node assay (LLNA) has been examined in relation to various chemical reaction mechanistic domains known to be associated with sensitization. It is demonstrated here that the dataset does cover the main reaction mechanistic domains. In addition, it is shown that assignment to a reaction mechanistic domain is a critical first step in a strategic approach to understanding, ultimately on a quantitative basis, how chemical properties influence the potency of skin sensitizing chemicals. This understanding is necessary if reliable non-animal approaches, including (quantitative) structure-activity relationships (Q)SARs, read-across, and experimental chemistry based models, are to be developed.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

Organophotocatalysis: Insights into the Mechanistic Aspects of Thiourea-Mediated Intermolecular [2+2] Photocycloadditions.

Science.gov (United States)

Vallavoju, Nandini; Selvakumar, Sermadurai; Pemberton, Barry C; Jockusch, Steffen; Sibi, Mukund P; Sivaguru, Jayaraman

2016-04-25

Mechanistic investigations of the intermolecular [2+2] photocycloaddition of coumarin with tetramethylethylene mediated by thiourea catalysts reveal that the reaction is enabled by a combination of minimized aggregation, enhanced intersystem crossing, and altered excited-state lifetime(s). These results clarify how the excited-state reactivity can be manipulated through catalyst-substrate interactions and reveal a third mechanistic pathway for thiourea-mediated organo-photocatalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Mechanistic Reliability Assessment of RVACS and Metal Fuel Inherent Reactivity Feedbacks

Energy Technology Data Exchange (ETDEWEB)

Grabaskas, David; Brunett, Acacia J.; Passerini, Stefano; Grelle, Austin

2017-09-24

GE Hitachi Nuclear Energy (GEH) and Argonne National Laboratory (Argonne) participated in a two year collaboration to modernize and update the probabilistic risk assessment (PRA) for the PRISM sodium fast reactor. At a high level, the primary outcome of the project was the development of a next-generation PRA that is intended to enable risk-informed prioritization of safety- and reliability-focused research and development. A central Argonne task during this project was a reliability assessment of passive safety systems, which included the Reactor Vessel Auxiliary Cooling System (RVACS) and the inherent reactivity feedbacks of the metal fuel core. Both systems were examined utilizing a methodology derived from the Reliability Method for Passive Safety Functions (RMPS), with an emphasis on developing success criteria based on mechanistic system modeling while also maintaining consistency with the Fuel Damage Categories (FDCs) of the mechanistic source term assessment. This paper provides an overview of the reliability analyses of both systems, including highlights of the FMEAs, the construction of best-estimate models, uncertain parameter screening and propagation, and the quantification of system failure probability. In particular, special focus is given to the methodologies to perform the analysis of uncertainty propagation and the determination of the likelihood of violating FDC limits. Additionally, important lessons learned are also reviewed, such as optimal sampling methodologies for the discovery of low likelihood failure events and strategies for the combined treatment of aleatory and epistemic uncertainties.

Fuel swelling importance in PCI mechanistic modelling

International Nuclear Information System (INIS)

Arimescu, V.I.

2005-01-01

Under certain conditions, fuel pellet swelling is the most important factor in determining the intensity of the pellet-to-cladding mechanical interaction (PCMI). This is especially true during power ramps, which lead to a temperature increase to a higher terminal plateau that is maintained for hours. The time-dependent gaseous swelling is proportional to temperature and is also enhanced by the increased gas atom migration to the grain boundary during the power ramp. On the other hand, gaseous swelling is inhibited by a compressive hydrostatic stress in the pellet. Therefore, PCMI is the net result of combining gaseous swelling and pellet thermal expansion with the opposing feedback from the cladding mechanical reaction. The coupling of the thermal and mechanical processes, mentioned above, with various feedback loops is best simulated by a mechanistic fuel code. This paper discusses a mechanistic swelling model that is coupled with a fission gas release model as well as a mechanical model of the fuel pellet. The role of fuel swelling is demonstrated for typical power ramps at different burn-ups. Also, fuel swelling plays a significant role in avoiding the thermal instability for larger gap fuel rods, by limiting the potentially exponentially increasing gap due to the positive feedback loop effect of increasing fission gas release and the associated over-pressure inside the cladding. (author)

Does Mechanistic Thinking Improve Student Success in Organic Chemistry?

Science.gov (United States)

Grove, Nathaniel P.; Cooper, Melanie M.; Cox, Elizabeth L.

2012-01-01

The use of the curved-arrow notation to depict electron flow during mechanistic processes is one of the most important representational conventions in the organic chemistry curriculum. Our previous research documented a disturbing trend: when asked to predict the products of a series of reactions, many students do not spontaneously engage in…

Existing pavement input information for the mechanistic-empirical pavement design guide.

Science.gov (United States)

2009-02-01

The objective of this study is to systematically evaluate the Iowa Department of Transportations (DOTs) existing Pavement Management Information System (PMIS) with respect to the input information required for Mechanistic-Empirical Pavement Des...

Mechanistic modeling of reactive soil nitrogen emissions across agricultural management practices

Science.gov (United States)

Rasool, Q. Z.; Miller, D. J.; Bash, J. O.; Venterea, R. T.; Cooter, E. J.; Hastings, M. G.; Cohan, D. S.

2017-12-01

The global reactive nitrogen (N) budget has increased by a factor of 2-3 from pre-industrial levels. This increase is especially pronounced in highly N fertilized agricultural regions in summer. The reactive N emissions from soil to atmosphere can be in reduced (NH3) or oxidized (NO, HONO, N2O) forms, depending on complex biogeochemical transformations of soil N reservoirs. Air quality models like CMAQ typically neglect soil emissions of HONO and N2O. Previously, soil NO emissions estimated by models like CMAQ remained parametric and inconsistent with soil NH3 emissions. Thus, there is a need to more mechanistically and consistently represent the soil N processes that lead to reactive N emissions to the atmosphere. Our updated approach estimates soil NO, HONO and N2O emissions by incorporating detailed agricultural fertilizer inputs from EPIC, and CMAQ-modeled N deposition, into the soil N pool. EPIC addresses the nitrification, denitrification and volatilization rates along with soil N pools for agricultural soils. Suitable updates to account for factors like nitrite (NO2-) accumulation not addressed in EPIC, will also be made. The NO and N2O emissions from nitrification and denitrification are computed mechanistically using the N sub-model of DAYCENT. These mechanistic definitions use soil water content, temperature, NH4+ and NO3- concentrations, gas diffusivity and labile C availability as dependent parameters at various soil layers. Soil HONO emissions found to be most probable under high NO2- availability will be based on observed ratios of HONO to NO emissions under different soil moistures, pH and soil types. The updated scheme will utilize field-specific soil properties and N inputs across differing manure management practices such as tillage. Comparison of the modeled soil NO emission rates from the new mechanistic and existing schemes against field measurements will be discussed. Our updated framework will help to predict the diurnal and daily variability

The Cardiopulmonary Effects of Ambient Air Pollution and Mechanistic Pathways: A Comparative Hierarchical Pathway Analysis

Science.gov (United States)

Thomas, Duncan C.; Zhang, Junfeng; Kipen, Howard M.; Rich, David Q.; Zhu, Tong; Huang, Wei; Hu, Min; Wang, Guangfa; Wang, Yuedan; Zhu, Ping; Lu, Shou-En; Ohman-Strickland, Pamela; Diehl, Scott R.; Eckel, Sandrah P.

2014-01-01

Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001) and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005). These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours) and the hemostasis pathway responds gradually over a 2–3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system. PMID:25502951

The cardiopulmonary effects of ambient air pollution and mechanistic pathways: a comparative hierarchical pathway analysis.

Directory of Open Access Journals (Sweden)

Ananya Roy

Full Text Available Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001 and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005. These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours and the hemostasis pathway responds gradually over a 2-3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system.

A Mechanistic Source Term Calculation for a Metal Fuel Sodium Fast Reactor

Energy Technology Data Exchange (ETDEWEB)

Grabaskas, David; Bucknor, Matthew; Jerden, James

2017-06-26

A mechanistic source term (MST) calculation attempts to realistically assess the transport and release of radionuclides from a reactor system to the environment during a specific accident sequence. The U.S. Nuclear Regulatory Commission (NRC) has repeatedly stated its expectation that advanced reactor vendors will utilize an MST during the U.S. reactor licensing process. As part of a project to examine possible impediments to sodium fast reactor (SFR) licensing in the U.S., an analysis was conducted regarding the current capabilities to perform an MST for a metal fuel SFR. The purpose of the project was to identify and prioritize any gaps in current computational tools, and the associated database, for the accurate assessment of an MST. The results of the study demonstrate that an SFR MST is possible with current tools and data, but several gaps exist that may lead to possibly unacceptable levels of uncertainty, depending on the goals of the MST analysis.

Profiling the biological activity of oxide nanomaterials with mechanistic models

NARCIS (Netherlands)

Burello, E.

2013-01-01

In this study we present three mechanistic models for profiling the potential biological and toxicological effects of oxide nanomaterials. The models attempt to describe the reactivity, protein adsorption and membrane adhesion processes of a large range of oxide materials and are based on properties

Generative Mechanistic Explanation Building in Undergraduate Molecular and Cellular Biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-01-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among…

Melanie Klein's metapsychology: phenomenological and mechanistic perspective.

Science.gov (United States)

Mackay, N

1981-01-01

Freud's metapsychology is the subject of an important debate. This is over whether psychoanalysis is best construed as a science of the natural science type or as a special human science. The same debate applies to Melanie Klein's work. In Klein's metapsychology are two different and incompatible models of explanation. One is taken over from Freud's structural theory and appears to be similarly mechanistic. The other is clinically based and phenomenological. These two are discussed with special reference to the concepts of "phantasy" and "internal object".

Mechanistic modelling of the corrosion behaviour of copper nuclear fuel waste containers

Energy Technology Data Exchange (ETDEWEB)

King, F; Kolar, M

1996-10-01

A mechanistic model has been developed to predict the long-term corrosion behaviour of copper nuclear fuel waste containers in a Canadian disposal vault. The model is based on a detailed description of the electrochemical, chemical, adsorption and mass-transport processes involved in the uniform corrosion of copper, developed from the results of an extensive experimental program. Predictions from the model are compared with the results of some of these experiments and with observations from a bronze cannon submerged in seawater saturated clay sediments. Quantitative comparisons are made between the observed and predicted corrosion potential, corrosion rate and copper concentration profiles adjacent to the corroding surface, as a way of validating the long-term model predictions. (author). 12 refs., 5 figs.

Further analysis of open-respirometry systems: an a-compartmental mechanistic approach

Directory of Open Access Journals (Sweden)

Chaui-Berlinck J.G.

2000-01-01

Full Text Available A system is said to be "instantaneous" when for a given constant input an equilibrium output is obtained after a while. In the meantime, the output is changing from its initial value towards the equilibrium one. This is the transient period of the system and transients are important features of open-respirometry systems. During transients, one cannot compute the input amplitude directly from the output. The existing models (e.g., first or second order dynamics cannot account for many of the features observed in real open-respirometry systems, such as time lag. Also, these models do not explain what should be expected when a system is speeded up or slowed down. The purpose of the present study was to develop a mechanistic approach to the dynamics of open-respirometry systems, employing basic thermodynamic concepts. It is demonstrated that all the main relevant features of the output dynamics are due to and can be adequately explained by a distribution of apparent velocities within the set of molecules travelling along the system. The importance of the rate at which the molecules leave the sensor is explored for the first time. The study approaches the difference in calibrating a system with a continuous input and with a "unit impulse": the former truly reveals the dynamics of the system while the latter represents the first derivative (in time of the former and, thus, cannot adequately be employed in the apparent time-constant determination. Also, we demonstrate why the apparent order of the output changes with volume or flow.

Cross-study and cross-omics comparisons of three nephrotoxic compounds reveal mechanistic insights and new candidate biomarkers

International Nuclear Information System (INIS)

Matheis, Katja A.; Com, Emmanuelle; Gautier, Jean-Charles; Guerreiro, Nelson; Brandenburg, Arnd; Gmuender, Hans; Sposny, Alexandra; Hewitt, Philip; Amberg, Alexander; Boernsen, Olaf; Riefke, Bjoern; Hoffmann, Dana; Mally, Angela; Kalkuhl, Arno; Suter, Laura; Dieterle, Frank; Staedtler, Frank

2011-01-01

The European InnoMed-PredTox project was a collaborative effort between 15 pharmaceutical companies, 2 small and mid-sized enterprises, and 3 universities with the goal of delivering deeper insights into the molecular mechanisms of kidney and liver toxicity and to identify mechanism-linked diagnostic or prognostic safety biomarker candidates by combining conventional toxicological parameters with 'omics' data. Mechanistic toxicity studies with 16 different compounds, 2 dose levels, and 3 time points were performed in male Crl: WI(Han) rats. Three of the 16 investigated compounds, BI-3 (FP007SE), Gentamicin (FP009SF), and IMM125 (FP013NO), induced kidney proximal tubule damage (PTD). In addition to histopathology and clinical chemistry, transcriptomics microarray and proteomics 2D-DIGE analysis were performed. Data from the three PTD studies were combined for a cross-study and cross-omics meta-analysis of the target organ. The mechanistic interpretation of kidney PTD-associated deregulated transcripts revealed, in addition to previously described kidney damage transcript biomarkers such as KIM-1, CLU and TIMP-1, a number of additional deregulated pathways congruent with histopathology observations on a single animal basis, including a specific effect on the complement system. The identification of new, more specific biomarker candidates for PTD was most successful when transcriptomics data were used. Combining transcriptomics data with proteomics data added extra value.

MycoCAP - Mycobacterium Comparative Analysis Platform.

Science.gov (United States)

Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V R; Wee, Wei Yee; Wong, Guat Jah

2015-12-15

Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my.

A mechanistic modelling and data assimilation approach to estimate the carbon/chlorophyll and carbon/nitrogen ratios in a coupled hydrodynamical-biological model

Directory of Open Access Journals (Sweden)

B. Faugeras

2004-01-01

Full Text Available The principal objective of hydrodynamical-biological models is to provide estimates of the main carbon fluxes such as total and export oceanic production. These models are nitrogen based, that is to say that the variables are expressed in terms of their nitrogen content. Moreover models are calibrated using chlorophyll data sets. Therefore carbon to chlorophyll (C:Chl and carbon to nitrogen (C:N ratios have to be assumed. This paper addresses the problem of the representation of these ratios. In a 1D framework at the DYFAMED station (NW Mediterranean Sea we propose a model which enables the estimation of the basic biogeochemical fluxes and in which the spatio-temporal variability of the C:Chl and C:N ratios is fully represented in a mechanical way. This is achieved through the introduction of new state variables coming from the embedding of a phytoplankton growth model in a more classical Redfieldian NNPZD-DOM model (in which the C:N ratio is assumed to be a constant. Following this modelling step, the parameters of the model are estimated using the adjoint data assimilation method which enables the assimilation of chlorophyll and nitrate data sets collected at DYFAMED in 1997.Comparing the predictions of the new Mechanistic model with those of the classical Redfieldian NNPZD-DOM model which was calibrated with the same data sets, we find that both models reproduce the reference data in a comparable manner. Both fluxes and stocks can be equally well predicted by either model. However if the models are coinciding on an average basis, they are diverging from a variability prediction point of view. In the Mechanistic model biology adapts much faster to its environment giving rise to higher short term variations. Moreover the seasonal variability in total production differs from the Redfieldian NNPZD-DOM model to the Mechanistic model. In summer the Mechanistic model predicts higher production values in carbon unit than the Redfieldian NNPZD

Pharmacokinetic and pharmacodynamic analysis comparing diverse effects of detomidine, medetomidine, and dexmedetomidine in the horse: a population analysis.

Science.gov (United States)

Grimsrud, K N; Ait-Oudhia, S; Durbin-Johnson, B P; Rocke, D M; Mama, K R; Rezende, M L; Stanley, S D; Jusko, W J

2015-02-01

The present study characterizes the pharmacokinetic (PK) and pharmacodynamic (PD) relationships of the α2-adrenergic receptor agonists detomidine (DET), medetomidine (MED) and dexmedetomidine (DEX) in parallel groups of horses from in vivo data after single bolus doses. Head height (HH), heart rate (HR), and blood glucose concentrations were measured over 6 h. Compartmental PK and minimal physiologically based PK (mPBPK) models were applied and incorporated into basic and extended indirect response models (IRM). Population PK/PD analysis was conducted using the Monolix software implementing the stochastic approximation expectation maximization algorithm. Marked reductions in HH and HR were found. The drug concentrations required to obtain inhibition at half-maximal effect (IC50 ) were approximately four times larger for DET than MED and DEX for both HH and HR. These effects were not gender dependent. Medetomidine had a greater influence on the increase in glucose concentration than DEX. The developed models demonstrate the use of mechanistic and mPBPK/PD models for the analysis of clinically obtainable in vivo data. © 2014 John Wiley & Sons Ltd.

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

Directory of Open Access Journals (Sweden)

Anshuman Dixit

2009-08-01

Full Text Available Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition

Use of mechanistic simulations as a quantitative risk-ranking tool within the quality by design framework.

Science.gov (United States)

Stocker, Elena; Toschkoff, Gregor; Sacher, Stephan; Khinast, Johannes G

2014-11-20

The purpose of this study is to evaluate the use of computer simulations for generating quantitative knowledge as a basis for risk ranking and mechanistic process understanding, as required by ICH Q9 on quality risk management systems. In this specific publication, the main focus is the demonstration of a risk assessment workflow, including a computer simulation for the generation of mechanistic understanding of active tablet coating in a pan coater. Process parameter screening studies are statistically planned under consideration of impacts on a potentially critical quality attribute, i.e., coating mass uniformity. Based on computer simulation data the process failure mode and effects analysis of the risk factors is performed. This results in a quantitative criticality assessment of process parameters and the risk priority evaluation of failure modes. The factor for a quantitative reassessment of the criticality and risk priority is the coefficient of variation, which represents the coating mass uniformity. The major conclusion drawn from this work is a successful demonstration of the integration of computer simulation in the risk management workflow leading to an objective and quantitative risk assessment. Copyright © 2014. Published by Elsevier B.V.

A mechanistic model on methane oxidation in the rice rhizosphere

NARCIS (Netherlands)

Bodegom, van P.M.; Leffelaar, P.A.; Goudriaan, J.

2001-01-01

A mechanistic model is presented on the processes leading to methane oxidation in rice rhizosphere. The model is driven by oxygen release from a rice root into anaerobic rice soil. Oxygen is consumed by heterotrophic and methanotrophic respiration, described by double Monod kinetics, and by iron

Mechanistic effect modeling for ecological risk assessment: where to go from here?

Science.gov (United States)

Grimm, Volker; Martin, Benjamin T

2013-07-01

Mechanistic effect models (MEMs) consider the mechanisms of how chemicals affect individuals and ecological systems such as populations and communities. There is an increasing awareness that MEMs have high potential to make risk assessment of chemicals more ecologically relevant than current standard practice. Here we discuss what kinds of MEMs are needed to improve scientific and regulatory aspects of risk assessment. To make valid predictions for a wide range of environmental conditions, MEMs need to include a sufficient amount of emergence, for example, population dynamics emerging from what individual organisms do. We present 1 example where the life cycle of individuals is described using Dynamic Energy Budget theory. The resulting individual-based population model is thus parameterized at the individual level but correctly predicts multiple patterns at the population level. This is the case for both control and treated populations. We conclude that the state-of-the-art in mechanistic effect modeling has reached a level where MEMs are robust and predictive enough to be used in regulatory risk assessment. Mechanistic effect models will thus be used to advance the scientific basis of current standard practice and will, if their development follows Good Modeling Practice, be included in a standardized way in future regulatory risk assessments. Copyright © 2013 SETAC.

[Mechanistic modelling allows to assess pathways of DNA lesion interactions underlying chromosome aberration formation].

Science.gov (United States)

Eĭdel'man, Iu A; Slanina, S V; Sal'nikov, I V; Andreev, S G

2012-12-01

The knowledge of radiation-induced chromosomal aberration (CA) mechanisms is required in many fields of radiation genetics, radiation biology, biodosimetry, etc. However, these mechanisms are yet to be quantitatively characterised. One of the reasons is that the relationships between primary lesions of DNA/chromatin/chromosomes and dose-response curves for CA are unknown because the pathways of lesion interactions in an interphase nucleus are currently inaccessible for direct experimental observation. This article aims for the comparative analysis of two principally different scenarios of formation of simple and complex interchromosomal exchange aberrations: by lesion interactions at chromosome territories' surface vs. in the whole space of the nucleus. The analysis was based on quantitative mechanistic modelling of different levels of structures and processes involved in CA formation: chromosome structure in an interphase nucleus, induction, repair and interactions of DNA lesions. It was shown that the restricted diffusion of chromosomal loci, predicted by computational modelling of chromosome organization, results in lesion interactions in the whole space of the nucleus being impossible. At the same time, predicted features of subchromosomal dynamics agrees well with in vivo observations and does not contradict the mechanism of CA formation at the surface of chromosome territories. On the other hand, the "surface mechanism" of CA formation, despite having certain qualities, proved to be insufficient to explain high frequency of complex exchange aberrations observed by mFISH technique. The alternative mechanism, CA formation on nuclear centres is expected to be sufficient to explain frequent complex exchanges.

Global scale analysis and evaluation of an improved mechanistic representation of plant nitrogen and carbon dynamics in the Community Land Model (CLM)

Science.gov (United States)

Ghimire, B.; Riley, W. J.; Koven, C. D.; Randerson, J. T.; Mu, M.; Kattge, J.; Rogers, A.; Reich, P. B.

2014-12-01

In many ecosystems, nitrogen is the most limiting nutrient for plant growth and productivity. However mechanistic representation of nitrogen uptake linked to root traits, and functional nitrogen allocation among different leaf enzymes involved in respiration and photosynthesis is currently lacking in Earth System models. The linkage between nitrogen availability and plant productivity is simplistically represented by potential photosynthesis rates, and is subsequently downregulated depending on nitrogen supply and other nitrogen consumers in the model (e.g., nitrification). This type of potential photosynthesis rate calculation is problematic for several reasons. Firstly, plants do not photosynthesize at potential rates and then downregulate. Secondly, there is considerable subjectivity on the meaning of potential photosynthesis rates. Thirdly, there exists lack of understanding on modeling these potential photosynthesis rates in a changing climate. In addition to model structural issues in representing photosynthesis rates, the role of plant roots in nutrient acquisition have been largely ignored in Earth System models. For example, in CLM4.5, nitrogen uptake is linked to leaf level processes (e.g., primarily productivity) rather than root scale process involved in nitrogen uptake. We present a new plant model for CLM with an improved mechanistic presentation of plant nitrogen uptake based on root scale Michaelis Menten kinetics, and stronger linkages between leaf nitrogen and plant productivity by inferring relationships observed in global databases of plant traits (including the TRY database and several individual studies). We also incorporate improved representation of plant nitrogen leaf allocation, especially in tropical regions where significant over-prediction of plant growth and productivity in CLM4.5 simulations exist. We evaluate our improved global model simulations using the International Land Model Benchmarking (ILAMB) framework. We conclude that

Mathematical Description and Mechanistic Reasoning: A Pathway toward STEM Integration

Science.gov (United States)

Weinberg, Paul J.

2017-01-01

Because reasoning about mechanism is critical to disciplined inquiry in science, technology, engineering, and mathematics (STEM) domains, this study focuses on ways to support the development of this form of reasoning. This study attends to how mechanistic reasoning is constituted through mathematical description. This study draws upon Smith's…

INCORPORATION OF MECHANISTIC INFORMATION IN THE ARSENIC PBPK MODEL DEVELOPMENT PROCESS

Science.gov (United States)

INCORPORATING MECHANISTIC INSIGHTS IN A PBPK MODEL FOR ARSENICElaina M. Kenyon, Michael F. Hughes, Marina V. Evans, David J. Thomas, U.S. EPA; Miroslav Styblo, University of North Carolina; Michael Easterling, Analytical Sciences, Inc.A physiologically based phar...

A metabonomic approach for mechanistic exploration of pre-clinical toxicology.

Science.gov (United States)

Coen, Muireann

2010-12-30

Metabonomics involves the application of advanced analytical tools to profile the diverse metabolic complement of a given biofluid or tissue. Subsequent statistical modelling of the complex multivariate spectral profiles enables discrimination between phenotypes of interest and identifies panels of discriminatory metabolites that represent candidate biomarkers. This review article presents an overview of recent developments in the field of metabonomics with a focus on application to pre-clinical toxicology studies. Recent research investigations carried out as part of the international COMET 2 consortium project on the hepatotoxic action of the aminosugar, galactosamine (galN) are presented. The application of advanced, high-field NMR spectroscopy is demonstrated, together with complementary application of a targeted mass spectrometry platform coupled with ultra-performance liquid chromatography. Much novel mechanistic information has been gleaned on both the mechanism of galN hepatotoxicity in multiple biofluids and tissues, and on the protection afforded by co-administration of glycine and uridine. The simultaneous identification of both the metabolic fate of galN and its associated endogenous consequences in spectral profiles is demonstrated. Furthermore, metabonomic assessment of inter-animal variability in response to galN presents enhanced mechanistic insight on variable response phentoypes and is relevant to understanding wider aspects of individual variability in drug response. This exemplar highlights the analytical and statistical tools commonly applied in metabonomic studies and notably, the approach is applicable to the study of any toxin/drug or intervention of interest. The metabonomic approach holds considerable promise and potential to significantly advance our understanding of the mechanistic bases for adverse drug reactions. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Mechanistic insights into nanotoxicity determined by synchrotron radiation-based Fourier-transform infrared imaging and multivariate analysis.

Science.gov (United States)

Riding, Matthew J; Trevisan, Júlio; Hirschmugl, Carol J; Jones, Kevin C; Semple, Kirk T; Martin, Francis L

2012-12-01

Our ability to identify the mechanisms by which carbon-based nanomaterials (CBNs) exert toxicity in cells is constrained by the lack of standardized methodologies to assay endpoint effects. Herein we describe a method of mechanistically identifying the effects of various CBN types in both prokaryotic and eukaryotic cells using multi-beam synchrotron radiation-based Fourier-transform infrared imaging (SR-FTIRI) at diffraction-limited resolution. This technique overcomes many of the inherent difficulties of assaying nanotoxicity and demonstrates exceptional sensitivity in identifying the effects of CBNs in cells at environmentally-relevant concentrations. We identify key mechanisms of nanotoxicity as the alteration of Amide and lipid biomolecules, but propose more specific bioactivity of CBNs occurs as a result of specific interactions between CBN structural conformation and cellular characteristics. Copyright © 2012 Elsevier Ltd. All rights reserved.

A mechanistic approach to postirradiation spoilage kinetics of fish

International Nuclear Information System (INIS)

Tukenmez, I.

2004-01-01

Full text: In order to simulate postirradiation spoilage of fish, the mechanistic aspects of the growth of surviving microorganisms during chill storage and their product formation in irradiated fish were analyzed. Anchovy (Engraulis encrasicholus) samples those unirradiated and irradiated at 1, 2 and 3 kGy doses of gamma radiation were stored at +2 o C for 21 days. Total bacterial counts (TBC) and trimethylamine (TMA) analysis of the samples were done periodically during storage. Depending on the proposed spoilage mechanism, kinetic model equations were derived. By using experimental data of TBC and TMA in the developed model, the postirradiation spoilage parameters including growth rate constant, inital and maximum attainable TBC, lag time and TMA yield were evaluated and microbial spoilage of fish was simulated for postirradiation storage. Shelf life of irradiated fish was estimated depending on the spoilage kinetics. Dose effects on the kinetic parameters were analyzed. It is suggested that the kinetic evaluation method developed in this study may be used for quality assessment, shelf life determination and dose optimization for radiation preservation of fish

Ruthenium-Catalyzed Transformations of Alcohols: Mechanistic Investigations and Methodology Development

DEFF Research Database (Denmark)

Makarov, Ilya; Madsen, Robert; Fristrup, Peter

with dimethoxyisopropylidene and pyridilidene ligands could be more active than RuCl2(IiPr)(p-cymene) used in the mechanistic investigation. Two analogs of the calculated complexes were synthesized but were not isolated in a pure form. The amidation reaction catalyzed by a mixture containing the N-ethyl pyridilidene...

Mechanistic investigation on the oxidation of kinetin by Ag(III)

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 122; Issue 6. Mechanistic investigation on the oxidation of kinetin by Ag(III) periodate complex in aqueous alkaline media: A kinetic approach. S D Lamani A M Tatagar S T Nandibewoor. Full Papers Volume 122 Issue 6 November 2010 pp 891-900 ...

A Comparative Study on Error Analysis

DEFF Research Database (Denmark)

Wu, Xiaoli; Zhang, Chun

2015-01-01

Title: A Comparative Study on Error Analysis Subtitle: - Belgian (L1) and Danish (L1) learners’ use of Chinese (L2) comparative sentences in written production Xiaoli Wu, Chun Zhang Abstract: Making errors is an inevitable and necessary part of learning. The collection, classification and analysis...... the occurrence of errors either in linguistic or pedagogical terms. The purpose of the current study is to demonstrate the theoretical and practical relevance of error analysis approach in CFL by investigating two cases - (1) Belgian (L1) learners’ use of Chinese (L2) comparative sentences in written production...... of errors in the written and spoken production of L2 learners has a long tradition in L2 pedagogy. Yet, in teaching and learning Chinese as a foreign language (CFL), only handful studies have been made either to define the ‘error’ in a pedagogically insightful way or to empirically investigate...

Comparing Results from Constant Comparative and Computer Software Methods: A Reflection about Qualitative Data Analysis

Science.gov (United States)

Putten, Jim Vander; Nolen, Amanda L.

2010-01-01

This study compared qualitative research results obtained by manual constant comparative analysis with results obtained by computer software analysis of the same data. An investigated about issues of trustworthiness and accuracy ensued. Results indicated that the inductive constant comparative data analysis generated 51 codes and two coding levels…

Development of a mechanistic model for prediction of CO2 capture from gas mixtures by amine solutions in porous membranes.

Science.gov (United States)

Ghadiri, Mehdi; Marjani, Azam; Shirazian, Saeed

2017-06-01

A mechanistic model was developed in order to predict capture and removal of CO 2 from air using membrane technology. The considered membrane was a hollow-fiber contactor module in which gas mixture containing CO 2 was assumed as feed while 2-amino-2-metyl-1-propanol (AMP) was used as an absorbent. The mechanistic model was developed according to transport phenomena taking into account mass transfer and chemical reaction between CO 2 and amine in the contactor module. The main aim of modeling was to track the composition and flux of CO 2 and AMP in the membrane module for process optimization. For modeling of the process, the governing equations were computed using finite element approach in which the whole model domain was discretized into small cells. To confirm the simulation findings, model outcomes were compared with experimental data and good consistency was revealed. The results showed that increasing temperature of AMP solution increases CO 2 removal in the hollow-fiber membrane contactor.

An improved mechanistic critical heat flux model for subcooled flow boiling

Energy Technology Data Exchange (ETDEWEB)

Kwon, Young Min [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Chang, Soon Heung [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

1998-12-31

Based on the bubble coalescence adjacent to the heated wall as a flow structure for CHF condition, Chang and Lee developed a mechanistic critical heat flux (CHF) model for subcooled flow boiling. In this paper, improvements of Chang-Lee model are implemented with more solid theoretical bases for subcooled and low-quality flow boiling in tubes. Nedderman-Shearer`s equations for the skin friction factor and universal velocity profile models are employed. Slip effect of movable bubbly layer is implemented to improve the predictability of low mass flow. Also, mechanistic subcooled flow boiling model is used to predict the flow quality and void fraction. The performance of the present model is verified using the KAIST CHF database of water in uniformly heated tubes. It is found that the present model can give a satisfactory agreement with experimental data within less than 9% RMS error. 9 refs., 5 figs. (Author)

An improved mechanistic critical heat flux model for subcooled flow boiling

Energy Technology Data Exchange (ETDEWEB)

Kwon, Young Min [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Chang, Soon Heung [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

1997-12-31

Based on the bubble coalescence adjacent to the heated wall as a flow structure for CHF condition, Chang and Lee developed a mechanistic critical heat flux (CHF) model for subcooled flow boiling. In this paper, improvements of Chang-Lee model are implemented with more solid theoretical bases for subcooled and low-quality flow boiling in tubes. Nedderman-Shearer`s equations for the skin friction factor and universal velocity profile models are employed. Slip effect of movable bubbly layer is implemented to improve the predictability of low mass flow. Also, mechanistic subcooled flow boiling model is used to predict the flow quality and void fraction. The performance of the present model is verified using the KAIST CHF database of water in uniformly heated tubes. It is found that the present model can give a satisfactory agreement with experimental data within less than 9% RMS error. 9 refs., 5 figs. (Author)

INTEGRATION OF QSAR AND SAR METHODS FOR THE MECHANISTIC INTERPRETATION OF PREDICTIVE MODELS FOR CARCINOGENICITY

Directory of Open Access Journals (Sweden)

Natalja Fjodorova

2012-07-01

Full Text Available The knowledge-based Toxtree expert system (SAR approach was integrated with the statistically based counter propagation artificial neural network (CP ANN model (QSAR approach to contribute to a better mechanistic understanding of a carcinogenicity model for non-congeneric chemicals using Dragon descriptors and carcinogenic potency for rats as a response. The transparency of the CP ANN algorithm was demonstrated using intrinsic mapping technique specifically Kohonen maps. Chemical structures were represented by Dragon descriptors that express the structural and electronic features of molecules such as their shape and electronic surrounding related to reactivity of molecules. It was illustrated how the descriptors are correlated with particular structural alerts (SAs for carcinogenicity with recognized mechanistic link to carcinogenic activity. Moreover, the Kohonen mapping technique enables one to examine the separation of carcinogens and non-carcinogens (for rats within a family of chemicals with a particular SA for carcinogenicity. The mechanistic interpretation of models is important for the evaluation of safety of chemicals.

Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation: Report of an FDA Public Workshop.

Science.gov (United States)

Zhang, X; Duan, J; Kesisoglou, F; Novakovic, J; Amidon, G L; Jamei, M; Lukacova, V; Eissing, T; Tsakalozou, E; Zhao, L; Lionberger, R

2017-08-01

On May 19, 2016, the US Food and Drug Administration (FDA) hosted a public workshop, entitled "Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation." The topic of mechanistic oral absorption modeling, which is one of the major applications of physiologically based pharmacokinetic (PBPK) modeling and simulation, focuses on predicting oral absorption by mechanistically integrating gastrointestinal transit, dissolution, and permeation processes, incorporating systems, active pharmaceutical ingredient (API), and the drug product information, into a systemic mathematical whole-body framework. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

Mechanistic species distribution modeling reveals a niche shift during invasion.

Science.gov (United States)

Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

2017-06-01

Niche shifts of nonnative plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by reanalyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially invaded ranges of individual populations. Northern-origin populations that were established outside the generally accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially invaded range northward and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

Lipids, adiposity and tendinopathy : is there a mechanistic link? Critical review

NARCIS (Netherlands)

Scott, Alex; Zwerver, Johannes; Grewal, Navi; de Sa, Agnetha; Alktebi, Thuraya; Granville, David J.; Hart, David A.

Being overweight or obese is associated with an elevated risk of tendon pathology. However, for sportspeople the epidemiological data linking weight or adiposity on one hand, and risk of tendon pathology on the other, are less consistent. Indeed, the mechanistic links between diet, adiposity and

Mechanistic and "natural" body metaphors and their effects on attitudes to hormonal contraception.

Science.gov (United States)

Walker, Susan

2012-01-01

A small, self-selected convenience sample of male and female contraceptive users in the United Kingdom (n = 34) were interviewed between 2006 and 2008 concerning their feelings about the body and their contraceptive attitudes and experiences. The interviewees were a sub-sample of respondents (n = 188) who completed a paper-based questionnaire on similar topics, who were recruited through a poster placed in a family planning clinic, web-based advertisements on workplace and university websites, and through direct approaches to social groups. The bodily metaphors used when discussing contraception were analyzed using an interpretative phenomenological analytical approach facilitated by Atlas.ti software. The dominant bodily metaphor was mechanistic (i.e.,"body as machine"). A subordinate but influential bodily metaphor was the "natural" body, which had connotations of connection to nature and a quasi-sacred bodily order. Interviewees drew upon this "natural" metaphorical image in the context of discussing their anxieties about hormonal contraception. Drawing upon a "natural," non-mechanistic body image in the context of contraceptive decision-making contributed to reluctance to use a hormonal form of contraception. This research suggests that clinicians could improve communication and advice about contraception by recognizing that some users may draw upon non-mechanistic body imagery.

Neutron activation analysis-comparative (NAAC)

International Nuclear Information System (INIS)

Zimmer, W.H.

1979-01-01

A software system for the reduction of comparative neutron activation analysis data is presented. Libraries are constructed to contain the elemental composition and isotopic nuclear data of an unlimited number of standards. Ratios to unknown sample data are performed by standard calibrations. Interfering peak corrections, second-order activation-product corrections, and deconvolution of multiplets are applied automatically. Passive gamma-energy analysis can be performed with the same software. 3 figures

The upper and lower limits of the mechanistic stoichiometry of mitochondrial oxidative phosphorylation. Stoichiometry of oxidative phosphorylation.

Science.gov (United States)

Beavis, A D; Lehninger, A L

1986-07-15

Determination of the intrinsic or mechanistic P/O ratio of oxidative phosphorylation is difficult because of the unknown magnitude of leak fluxes. Applying a new approach developed to overcome this problem (see our preceding paper in this journal), the relationships between the rate of O2 uptake [( Jo)3], the net rate of phosphorylation (Jp), the P/O ratio, and the respiratory control ratio (RCR) have been determined in rat liver mitochondria when the rate of phosphorylation was systematically varied by three specific means. (a) When phosphorylation is titrated with carboxyatractyloside, linear relationships are observed between Jp and (Jo)3. These data indicate that the upper limit of the mechanistic P/O ratio is 1.80 for succinate and 2.90 for 3-hydroxybutyrate oxidation. (b) Titration with malonate or antimycin yields linear relationships between Jp and (Jo)3. These data give the lower limit of the mechanistic P/O ratio of 1.63 for succinate and 2.66 for 3-hydroxybutyrate oxidation. (c) Titration with a protonophore yields linear relationships between Jp, (Jo)3, and (Jo)4 and between P/O and 1/RCR. Extrapolation of the P/O ratio to 1/RCR = 0 yields P/O ratios of 1.75 for succinate and 2.73 for 3-hydroxybutyrate oxidation which must be equal to or greater than the mechanistic stoichiometry. When published values for the H+/O and H+/ATP ejection ratios are taken into consideration, these measurements suggest that the mechanistic P/O ratio is 1.75 for succinate oxidation and 2.75 for NADH oxidation.

Development of boiling transition analysis code TCAPE-INS/B based on mechanistic methods for BWR fuel bundles. Models and validations with boiling transition experimental data

International Nuclear Information System (INIS)

Ishida, Naoyuki; Utsuno, Hideaki; Kasahara, Fumio

2003-01-01

The Boiling Transition (BT) analysis code TCAPE-INS/B based on the mechanistic methods coupled with subchannel analysis has been developed for the evaluation of the integrity of Boiling Water Reactor (BWR) fuel rod bundles under abnormal operations. Objective of the development is the evaluation of the BT without using empirical BT and rewetting correlations needed for different bundle designs in the current analysis methods. TCAPE-INS/B consisted mainly of the drift-flux model, the film flow model, the cross-flow model, the thermal conductivity model and the heat transfer correlations. These models were validated systematically with the experimental data. The accuracy of the prediction for the steady-state Critical Heat Flux (CHF) and the transient temperature of the fuel rod surface after the occurrence of BT were evaluated on the validations. The calculations for the experiments with the single tube and bundles were carried out for the validations of the models incorporated in the code. The results showed that the steady-state CHF was predicted within about 6% average error. In the transient calculations, BT timing and temperature of the fuel rod surface gradient agreed well with experimental results, but rewetting was predicted lately. So, modeling of heat transfer phenomena during post-BT is under modification. (author)

Mutual Dependence Between Sedimentary Organic Carbon and Infaunal Macrobenthos Resolved by Mechanistic Modeling

Science.gov (United States)

Zhang, Wenyan; Wirtz, Kai

2017-10-01

The mutual dependence between sedimentary total organic carbon (TOC) and infaunal macrobenthos is here quantified by a mechanistic model. The model describes (i) the vertical distribution of infaunal macrobenthic biomass resulting from a trade-off between nutritional benefit (quantity and quality of TOC) and the costs of burial (respiration) and mortality, and (ii) the variable vertical distribution of TOC being in turn shaped by bioturbation of local macrobenthos. In contrast to conventional approaches, our model emphasizes variations of bioturbation both spatially and temporally depending on local food resources and macrobenthic biomass. Our implementation of the dynamic interaction between TOC and infaunal macrobenthos is able to capture a temporal benthic response to both depositional and erosional environments and provides improved estimates of the material exchange flux at the sediment-water interface. Applications to literature data for the North Sea demonstrate the robustness and accuracy of the model and its potential as an analysis tool for the status of TOC and macrobenthos in marine sediments. Results indicate that the vertical distribution of infaunal biomass is shaped by both the quantity and the quality of OC, while the community structure is determined only by the quality of OC. Bioturbation intensity may differ by 1 order of magnitude over different seasons owing to variations in the OC input, resulting in a significant modulation on the distribution of OC. Our relatively simple implementation may further improve models of early diagenesis and marine food web dynamics by mechanistically connecting the vertical distribution of both TOC and macrobenthic biomass.

Exploring the pros and cons of mechanistic case diagrams for problem-based learning

Directory of Open Access Journals (Sweden)

Minjeong Kim

2017-09-01

Full Text Available Purpose Mechanistic case diagram (MCD was recommended for increasing the depth of understanding of disease, but with few articles on its specific methods. We address the experience of making MCD in the fullest depth to identify the pros and cons of using MCDs in such ways. Methods During problem-based learning, we gave guidelines of MCD for its mechanistic exploration from subcellular processes to clinical features, being laid out in as much detail as possible. To understand the students’ attitudes and depth of study using MCDs, we analyzed the results of a questionnaire in an open format about experiencing MCDs and examined the resulting products. Results Through the responses to questionnaire, we found several favorable outcomes, major of which was deeper insight and comprehensive understanding of disease facilitated by the process of making well-organized diagram. The main disadvantages of these guidelines were the feeling of too much workload and difficulty of finding mechanisms. Students gave suggestions to overcome these problems: cautious reading of comprehensive texts, additional guidance from staff about depth and focus of mechanisms, and cooperative group work. From the analysis of maps, we recognized there should be allowance of diversities in the appearance of maps and many hypothetical connections, which could be related to an insufficient understanding of mechanisms in nature. Conclusion The more detailed an MCD task is, the better students can become acquainted with deep knowledges. However, this advantage should be balanced by the results that there are many ensuing difficulties for the work and deliberate help plans should be prepared.

Mechanistic-empirical subgrade design model based on heavy vehicle simulator test results

CSIR Research Space (South Africa)

Theyse, HL

2006-06-01

Full Text Available Although Accelerated Pavement Testing (APT) is often done with specific objectives, valuable pavement performance data is generated over the long-term that may be used to investigate pavement behaviour in general and calibrate mechanistic...

Identifying mechanistic similarities in drug responses

KAUST Repository

Zhao, C.

2012-05-15

Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

Prediction of warfarin maintenance dose in Han Chinese patients using a mechanistic model based on genetic and non-genetic factors.

Science.gov (United States)

Lu, Yuan; Yang, Jinbo; Zhang, Haiyan; Yang, Jin

2013-07-01

 = 186). In addition, *1/*1 patients needed about 1 week to reach steady state, whereas *1/*3 patients needed about 2 weeks. In terms of the predicted INRss values, only ten patients had INRss values outside the expected therapeutic range (1.5-2.8). To evaluate our mechanistic model, we predicted the warfarin maintenance dose for 183 patients and explained 42 % of its variation, which is comparable to our previous prediction using a descriptive model based on multiple linear regression. The mean predicted/observed warfarin doses (mg/day) for different combinations of CYP2C9 and VKORC1 genotypes were 1.54/3.75 (n = 1) for *1/*1 and GG, 3.33/3.66 (n = 36) for *1/*1 and AG, 2.31/2.41 (n = 136) for *1/*1 and AA, and 1.56/1.69 (n = 10) for *1/*3 and AA, respectively. Sensitivity analysis indicated BW and genetic polymorphisms of CYP2C9 and VKORC1 were important factors affecting the warfarin maintenance dose in the study population. The mechanistic model reported is the first to integrate IVIVE with a pharmacokinetic-pharmacodynamic model to describe the association of the warfarin maintenance dose with sex, age, BW and the genotypes of CYP2C9 and VKORC1. The model was effective in predicting S-warfarin clearance and in simulating its plasma concentration-time curve in a cohort of Han Chinese patients. In addition, the model accurately predicted the INR response and warfarin maintenance dose in a cohort of Han Chinese patients.

New web-based applications for mechanistic case diagramming

Directory of Open Access Journals (Sweden)

Fred R. Dee

2014-07-01

Full Text Available The goal of mechanistic case diagraming (MCD is to provide students with more in-depth understanding of cause and effect relationships and basic mechanistic pathways in medicine. This will enable them to better explain how observed clinical findings develop from preceding pathogenic and pathophysiological events. The pedagogic function of MCD is in relating risk factors, disease entities and morphology, signs and symptoms, and test and procedure findings in a specific case scenario with etiologic pathogenic and pathophysiological sequences within a flow diagram. In this paper, we describe the addition of automation and predetermined lists to further develop the original concept of MCD as described by Engelberg in 1992 and Guerrero in 2001. We demonstrate that with these modifications, MCD is effective and efficient in small group case-based teaching for second-year medical students (ratings of ~3.4 on a 4.0 scale. There was also a significant correlation with other measures of competency, with a ‘true’ score correlation of 0.54. A traditional calculation of reliability showed promising results (α =0.47 within a low stakes, ungraded environment. Further, we have demonstrated MCD's potential for use in independent learning and TBL. Future studies are needed to evaluate MCD's potential for use in medium stakes assessment or self-paced independent learning and assessment. MCD may be especially relevant in returning students to the application of basic medical science mechanisms in the clinical years.

Gradient matching methods for computational inference in mechanistic models for systems biology: a review and comparative analysis

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Benn eMacdonald

2015-11-01

Full Text Available Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs, is a challenging problem in contemporary systems biology. Conventional methods involve repeatedly solving the ODEs by numerical integration, which is computationally onerous and does not scale up to complex systems. Aimed at reducing the computational costs, new concepts based on gradient matching have recently been proposed in the computational statistics and machine learning literature. In a preliminary smoothing step, the time series data are interpolated; then, in a second step, the parameters of the ODEs are optimised so as to minimise some metric measuring the difference between the slopes of the tangents to the interpolants, and the time derivatives from the ODEs. In this way, the ODEs never have to be solved explicitly. This review provides a concise methodological overview of the current state-of-the-art methods for gradient matching in ODEs, followed by an empirical comparative evaluation based on a set of widely used and representative benchmark data.

p-adic analysis compared with real

CERN Document Server

Katok, Svetlana

2007-01-01

The book gives an introduction to p-adic numbers from the point of view of number theory, topology, and analysis. Compared to other books on the subject, its novelty is both a particularly balanced approach to these three points of view and an emphasis on topics accessible to undergraduates. In addition, several topics from real analysis and elementary topology which are not usually covered in undergraduate courses (totally disconnected spaces and Cantor sets, points of discontinuity of maps and the Baire Category Theorem, surjectivity of isometries of compact metric spaces) are also included in the book. They will enhance the reader's understanding of real analysis and intertwine the real and p-adic contexts of the book. The book is based on an advanced undergraduate course given by the author. The choice of the topic was motivated by the internal beauty of the subject of p-adic analysis, an unusual one in the undergraduate curriculum, and abundant opportunities to compare it with its much more familiar real...

Comparative analysis of traditional and alternative energy sources

Directory of Open Access Journals (Sweden)

Adriana Csikósová

2008-11-01

Full Text Available The presented thesis with designation of Comparing analysis of traditional and alternative energy resources includes, on basisof theoretical information source, research in firm, internal data, trends in company development and market, descriptionof the problem and its application. Theoretical information source is dedicated to the traditional and alternative energy resources,reserves of it, trends in using and development, the balance of it in the world, EU and in Slovakia as well. Analysis of the thesisis reflecting profile of the company and the thermal pump market evaluation using General Electric method. While the companyis implementing, except other products, the thermal pumps on geothermal energy base and surround energy base (air, the missionof the comparing analysis is to compare traditional energy resources with thermal pump from the ecological, utility and economic sideof it. The results of the comparing analysis are resumed in to the SWOT analysis. The part of the thesis includes he questionnaire offerfor effectiveness improvement and customer satisfaction analysis, and expected possibilities of alternative energy resources assistance(benefits from the government and EU funds.

Mechanistic model for Sr and Ba release from severely damaged fuel

International Nuclear Information System (INIS)

Rest, J.; Cronenberg, A.W.

1985-11-01

Among radionuclides associated with fission product release during severe accidents, the primary ones with health consequences are the volatile species of I, Te, and Cs, and the next most important are Sr, Ba, and Ru. Considerable progress has been made in the mechanistic understanding of I, Cs, Te, and noble gas release; however, no capability presently exists for estimating the release of Sr, Ba, and Ru. This paper presents a description of the primary physical/chemical models recently incorporated into the FASTGRASS-VFP (volatile fission product) code for the estimation of Sr and Ba release. FASTGRASS-VFP release predictions are compared with two data sets: (1) data from out-of-reactor induction-heating experiments on declad low-burnup (1000 and 4000 MWd/t) pellets, and (2) data from the more recent in-reactor PBF Severe Fuel Damage Tests, in which one-meter-long, trace-irradiated (89 MWd/t) and normally irradiated (approx.35,000 MWd/t) fuel rods were tested under accident conditions. 10 refs

Comparative analysis of Carnaval II Library

International Nuclear Information System (INIS)

Santos Bastos, W. dos

1981-01-01

The Carnaval II cross sections library from the french fast reactor calculation system is evaluated in two ways: 1 0 ) a comparative analysis of the calculations system for fast reactors at IEN (Instituto de Engenharia Nuclear) using a 'benchmark' model is done; 2 0 ) a comparative analysis in relation to the french system itself is also done, using calculations realized with two versions of the french library: the SETR-II and the CARNAVAL IV, the first one being anterior and the second one posterior to the Carnaval II version, the one used by IEN. (Author) [pt

Permanent deformation testing for a new South African mechanistic pavement design method

CSIR Research Space (South Africa)

Anochie-Boateng, Joseph

2012-01-01

Full Text Available The South Africa National Road Agency Limited together with the CSIR are undertaking a research and development project to support the revision of the South African mechanistic-empirical pavement design method. An important part of this project...

The use of mechanistic descriptions of algal growth and zooplankton grazing in an estuarine eutrophication model

Science.gov (United States)

Baird, M. E.; Walker, S. J.; Wallace, B. B.; Webster, I. T.; Parslow, J. S.

2003-03-01

A simple model of estuarine eutrophication is built on biomechanical (or mechanistic) descriptions of a number of the key ecological processes in estuaries. Mechanistically described processes include the nutrient uptake and light capture of planktonic and benthic autotrophs, and the encounter rates of planktonic predators and prey. Other more complex processes, such as sediment biogeochemistry, detrital processes and phosphate dynamics, are modelled using empirical descriptions from the Port Phillip Bay Environmental Study (PPBES) ecological model. A comparison is made between the mechanistically determined rates of ecological processes and the analogous empirically determined rates in the PPBES ecological model. The rates generally agree, with a few significant exceptions. Model simulations were run at a range of estuarine depths and nutrient loads, with outputs presented as the annually averaged biomass of autotrophs. The simulations followed a simple conceptual model of eutrophication, suggesting a simple biomechanical understanding of estuarine processes can provide a predictive tool for ecological processes in a wide range of estuarine ecosystems.

Oxidation of alginate and pectate biopolymers by cerium(IV) in perchloric and sulfuric acid solutions: A comparative kinetic and mechanistic study.

Science.gov (United States)

Fawzy, Ahmed

2016-03-15

The kinetics of oxidation of alginate (Alg) and pectate (Pec) carbohydrate biopolymers was studied by spectrophotometry in aqueous perchloric and sulfuric acid solutions at fixed ionic strengths and temperature. In both acids, the reactions showed a first order dependence on [Ce(IV)], whereas the orders with respect to biopolymer concentrations are less than unity. In perchloric acid, the reactions exhibited less than unit orders with respect to [H(+)] whereas those proceeded in sulfuric acid showed negative fractional-first order dependences on [H(+)]. The effect of ionic strength and dielectric constant was studied. Probable mechanistic schemes for oxidation reactions were proposed. In both acids, the final oxidation products were characterized as mono-keto derivatives of both biopolymers. The activation parameters with respect to the slow step of the mechanisms were computed and discussed. The rate laws were derived and the reaction constants involved in the different steps of the mechanisms were calculated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanistic model of mass-specific basal metabolic rate: evaluation in healthy young adults.

Science.gov (United States)

Wang, Z; Bosy-Westphal, A; Schautz, B; Müller, M

2011-12-01

Mass-specific basal metabolic rate (mass-specific BMR), defined as the resting energy expenditure per unit body mass per day, is an important parameter in energy metabolism research. However, a mechanistic explanation for magnitude of mass-specific BMR remains lacking. The objective of the present study was to validate the applicability of a proposed mass-specific BMR model in healthy adults. A mechanistic model was developed at the organ-tissue level, mass-specific BMR = Σ( K i × F i ), where Fi is the fraction of body mass as individual organs and tissues, and K i is the specific resting metabolic rate of major organs and tissues. The Fi values were measured by multiple MRI scans and the K i values were suggested by Elia in 1992. A database of healthy non-elderly non-obese adults (age 20 - 49 yrs, BMI BMR of all subjects was 21.6 ± 1.9 (mean ± SD) and 21.7 ± 1.6 kcal/kg per day, respectively. The measured mass-specific BMR was correlated with the predicted mass-specific BMR (r = 0.82, P BMR, versus the average of measured and predicted mass-specific BMR. In conclusion, the proposed mechanistic model was validated in non-elderly non-obese adults and can help to understand the inherent relationship between mass-specific BMR and body composition.

The coefficient of restitution of pressurized balls: a mechanistic model

Science.gov (United States)

Georgallas, Alex; Landry, Gaëtan

2016-01-01

Pressurized, inflated balls used in professional sports are regulated so that their behaviour upon impact can be anticipated and allow the game to have its distinctive character. However, the dynamics governing the impacts of such balls, even on stationary hard surfaces, can be extremely complex. The energy transformations, which arise from the compression of the gas within the ball and from the shear forces associated with the deformation of the wall, are examined in this paper. We develop a simple mechanistic model of the dependence of the coefficient of restitution, e, upon both the gauge pressure, P_G, of the gas and the shear modulus, G, of the wall. The model is validated using the results from a simple series of experiments using three different sports balls. The fits to the data are extremely good for P_G > 25 kPa and consistent values are obtained for the value of G for the wall material. As far as the authors can tell, this simple, mechanistic model of the pressure dependence of the coefficient of restitution is the first in the literature. *%K Coefficient of Restitution, Dynamics, Inflated Balls, Pressure, Impact Model

Students' Interpretations of Mechanistic Language in Organic Chemistry before Learning Reactions

Science.gov (United States)

Galloway, Kelli R.; Stoyanovich, Carlee; Flynn, Alison B.

2017-01-01

Research on mechanistic thinking in organic chemistry has shown that students attribute little meaning to the electron-pushing (i.e., curved arrow) formalism. At the University of Ottawa, a new curriculum has been developed in which students are taught the electron-pushing formalism prior to instruction on specific reactions--this formalism is…

Embedded Hyperchaotic Generators: A Comparative Analysis

Science.gov (United States)

Sadoudi, Said; Tanougast, Camel; Azzaz, Mohamad Salah; Dandache, Abbas

In this paper, we present a comparative analysis of FPGA implementation performances, in terms of throughput and resources cost, of five well known autonomous continuous hyperchaotic systems. The goal of this analysis is to identify the embedded hyperchaotic generator which leads to designs with small logic area cost, satisfactory throughput rates, low power consumption and low latency required for embedded applications such as secure digital communications between embedded systems. To implement the four-dimensional (4D) chaotic systems, we use a new structural hardware architecture based on direct VHDL description of the forth order Runge-Kutta method (RK-4). The comparative analysis shows that the hyperchaotic Lorenz generator provides attractive performances compared to that of others. In fact, its hardware implementation requires only 2067 CLB-slices, 36 multipliers and no block RAMs, and achieves a throughput rate of 101.6 Mbps, at the output of the FPGA circuit, at a clock frequency of 25.315 MHz with a low latency time of 316 ns. Consequently, these good implementation performances offer to the embedded hyperchaotic Lorenz generator the advantage of being the best candidate for embedded communications applications.

Mechanistic model to predict colostrum intake based on deuterium oxide dilution technique data and impact of gestation and prefarrowing diets on piglet intake and sow yield of colostrum.

Science.gov (United States)

Theil, P K; Flummer, C; Hurley, W L; Kristensen, N B; Labouriau, R L; Sørensen, M T

2014-12-01

The aims of the present study were to quantify colostrum intake (CI) of piglets using the D2O dilution technique, to develop a mechanistic model to predict CI, to compare these data with CI predicted by a previous empirical predictive model developed for bottle-fed piglets, and to study how composition of diets fed to gestating sows affected piglet CI, sow colostrum yield (CY), and colostrum composition. In total, 240 piglets from 40 litters were enriched with D2O. The CI measured by D2O from birth until 24 h after the birth of first-born piglet was on average 443 g (SD 151). Based on measured CI, a mechanistic model to predict CI was developed using piglet characteristics (24-h weight gain [WG; g], BW at birth [BWB; kg], and duration of CI [D; min]: CI, g=-106+2.26 WG+200 BWB+0.111 D-1,414 WG/D+0.0182 WG/BWB (R2=0.944). This model was used to predict the CI for all colostrum suckling piglets within the 40 litters (n=500, mean=437 g, SD=153 g) and was compared with the CI predicted by a previous empirical predictive model (mean=305 g, SD=140 g). The previous empirical model underestimated the CI by 30% compared with that obtained by the new mechanistic model. The sows were fed 1 of 4 gestation diets (n=10 per diet) based on different fiber sources (low fiber [17%] or potato pulp, pectin residue, or sugarbeet pulp [32 to 40%]) from mating until d 108 of gestation. From d 108 of gestation until parturition, sows were fed 1 of 5 prefarrowing diets (n=8 per diet) varying in supplemented fat (3% animal fat, 8% coconut oil, 8% sunflower oil, 8% fish oil, or 4% fish oil+4% octanoic acid). Sows fed diets with pectin residue or sugarbeet pulp during gestation produced colostrum with lower protein, fat, DM, and energy concentrations and higher lactose concentrations, and their piglets had greater CI as compared with sows fed potato pulp or the low-fiber diet (Pcoconut oil decreased lactose and increased DM concentrations of colostrum compared with other prefarrowing diets (P

Mechanistic models for the evaluation of biocatalytic reaction conditions and biosensor design optimization

DEFF Research Database (Denmark)

Semenova, Daria

. In the first case study a mechanistic model was developed to describe the enzymatic reaction of glucose oxidase and glucose in the presence of catalase inside a commercial microfluidic platform with integrated oxygen sensor spots. The simplicity of the proposed model allowed an easy calibration of the reaction...... the microfluidic device. In the second case study the flexible microfluidic platform with integrated amperometric glucose biosensors was developed for continuous monitoring of glucose consumption rates. The integration of the mixing chamber inside the platform allowed performing sample dilutions which subsequently......BRs. In the third case study the mechanistic model of the cyclic voltammetry response of the first generation glucose biosensors was developed and applied for the biosensor design optimization. Furthermore the obtained qualitative and quantitative dependencies between the model output and experimental results were...

Atomization of bismuthane in a dielectric barrier discharge: A mechanistic study

Czech Academy of Sciences Publication Activity Database

Kratzer, Jan; Zelina, Ondřej; Svoboda, Milan; Sturgeon, R. E.; Mester, Z.; Dědina, Jiří

2016-01-01

Roč. 88, č. 3 (2016), s. 1804-1811 ISSN 0003-2700 R&D Projects: GA ČR GA14-23532S Grant - others:GA AV ČR(CZ) M200311202 Institutional support: RVO:68081715 Keywords : dielectric barrier discharge * hydride generation * mechanistic study Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 6.320, year: 2016

Atomization of bismuthane in a dielectric barrier discharge: A mechanistic study

Czech Academy of Sciences Publication Activity Database

Kratzer, Jan; Zelina, Ondřej; Svoboda, Milan; Sturgeon, R. E.; Mester, Z.; Dědina, Jiří

2016-01-01

Roč. 88, č. 3 (2016), s. 1804-1811 ISSN 0003-2700 R&D Projects: GA ČR GA14-23532S Grant - others:GA AV ČR(CZ) M200311202 Institutional support: RVO:68081715 Keywords : dielectric barrier discharge * hydride generation * mechanistic study Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 6.320, year: 2016

From Source to Sink: Mechanistic Reasoning Using the Electron-Pushing Formalism

Science.gov (United States)

Bhattacharyya, Gautam

2013-01-01

Since the introduction of Morrison and Boyd's textbook in organic chemistry over 50 years ago, reaction mechanisms and mechanistic reasoning using the electron-pushing formalism (EPF) have become a mainstay of organic chemistry courses. In recent years there have even been several papers in this Journal and others detailing research on how…

Comparing methods of classifying life courses: Sequence analysis and latent class analysis

NARCIS (Netherlands)

Elzinga, C.H.; Liefbroer, Aart C.; Han, Sapphire

2017-01-01

We compare life course typology solutions generated by sequence analysis (SA) and latent class analysis (LCA). First, we construct an analytic protocol to arrive at typology solutions for both methodologies and present methods to compare the empirical quality of alternative typologies. We apply this

Comparing methods of classifying life courses: sequence analysis and latent class analysis

NARCIS (Netherlands)

Han, Y.; Liefbroer, A.C.; Elzinga, C.

2017-01-01

We compare life course typology solutions generated by sequence analysis (SA) and latent class analysis (LCA). First, we construct an analytic protocol to arrive at typology solutions for both methodologies and present methods to compare the empirical quality of alternative typologies. We apply this

Mechanistic Insight into the Dehydro-Diels-Alder Reaction of Styrene-Ynes.

Science.gov (United States)

Kocsis, Laura S; Kagalwala, Husain N; Mutto, Sharlene; Godugu, Bhaskar; Bernhard, Stefan; Tantillo, Dean J; Brummond, Kay M

2015-12-04

The Diels-Alder reaction represents one of the most thoroughly studied and well-understood synthetic transformations for the assembly of six-membered rings. Although intramolecular dehydro-Diels-Alder (IMDDA) reactions have previously been employed for the preparation of naphthalene and dihydronaphthalene substrates, low yields and product mixtures have reduced the impact and scope of this reaction. Through the mechanistic studies described within, we have confirmed that the thermal IMDDA reaction of styrene-ynes produces a naphthalene product via loss of hydrogen gas from the initially formed cycloadduct, a tetraenyl intermediate. Alternatively, the dihydronaphthalene product is afforded from the same tetraenyl intermediate via a radical isomerization process. Moreover, we have identified conditions that can be used to achieve efficient, high-yielding, and selective IMDDA reactions of styrene-ynes to form either naphthalene or dihydronaphthalene products. The operational simplicity and retrosynthetic orthogonality of this method for the preparation of naphthalenes and dihydronaphthalenes makes this transformation appealing for the synthesis of medicinal and material targets. The mechanistic studies within may impact the development of other thermal transformations.

Nuclear power ecology: comparative analysis

International Nuclear Information System (INIS)

Trofimenko, A.P.; Lips'ka, A.Yi.; Pisanko, Zh.Yi.

2005-01-01

Ecological effects of different energy sources are compared. Main actions for further nuclear power development - safety increase and waste management, are noted. Reasons of restrained public position to nuclear power and role of social and political factors in it are analyzed. An attempt is undertaken to separate real difficulties of nuclear power from imaginary ones that appear in some mass media. International actions of environment protection are noted. Risk factors at different energy source using are compared. The results of analysis indicate that ecological influence and risk for nuclear power are of minimum

Respiratory cancer risks associated with low-level nickel exposure: an integrated assessment based on animal, epidemiological, and mechanistic data.

Science.gov (United States)

Seilkop, Steven K; Oller, Adriana R

2003-04-01

Increased lung and nasal cancer risks have been reported in several cohorts of nickel refinery workers, but in more than 90% of the nickel-exposed workers that have been studied there is little, if any evidence of excess risk. This investigation utilizes human exposure measurements, animal data from cancer bioassays of three nickel compounds, and a mechanistic theory of nickel carcinogenesis to reconcile the disparities in lung cancer risk among nickel-exposed workers. Animal data and mechanistic theory suggest that the apparent absence of risk in workers with low nickel exposures is due to threshold-like responses in lung tumor incidence (oxidic nickel), tumor promotion (soluble nickel), and genetic damage (sulfidic nickel). When animal-based lung cancer dose-response functions for these compounds are extrapolated to humans, taking into account interspecies differences in deposition and clearance, differences in particle size distributions, and human work activity patterns, the predicted risks at occupational exposures are remarkably similar to those observed in nickel-exposed workers. This provides support for using the animal-based dose-response functions to estimate occupational exposure limits, which are found to be comparable to those in current use.

Mechanistic-Empirical (M-E) Design Implementation & Monitoring for Flexible Pavements : 2018 PROJECT SUMMARY

Science.gov (United States)

2018-06-01

This document is a summary of the tasks performed for Project ICT-R27-149-1. Mechanistic-empirical (M-E)based flexible pavement design concepts and procedures were previously developed in Illinois Cooperative Highway Research Program projects IHR-...

Exploring BSEP Inhibition-Mediated Toxicity with a Mechanistic Model of Drug-Induced Liver Injury

Directory of Open Access Journals (Sweden)

Jeffrey L Woodhead

2014-11-01

Full Text Available Inhibition of the bile salt export pump (BSEP has been linked to incidence of drug-induced liver injury (DILI, presumably by the accumulation of toxic bile acids in the liver. We have previously constructed and validated a model of bile acid disposition within DILIsym®, a mechanistic model of DILI. In this paper, we use DILIsym® to simulate the DILI response of the hepatotoxic BSEP inhibitors bosentan and CP-724,714 and the non-hepatotoxic BSEP inhibitor telmisartan in humans in order to explore whether we can predict that hepatotoxic BSEP inhibitors can cause bile acid accumulation to reach toxic levels. We also simulate bosentan in rats in order to illuminate potential reasons behind the lack of toxicity in rats compared to the toxicity observed in humans. DILIsym® predicts that bosentan, but not telmisartan, will cause mild hepatocellular ATP decline and serum ALT elevation in a simulated population of humans. The difference in hepatotoxic potential between bosentan and telmisartan is consistent with clinical observations. However, DILIsym® underpredicts the incidence of bosentan toxicity. DILIsym® also predicts that bosentan will not cause toxicity in a simulated population of rats, and that the difference between the response to bosentan in rats and in humans is primarily due to the less toxic bile acid pool in rats. Our simulations also suggest a potential synergistic role for bile acid accumulation and mitochondrial electron transport chain inhibition in producing the observed toxicity in CP-724,714, and suggest that CP-724,714 metabolites may also play a role in the observed toxicity. Our work also compares the impact of competitive and noncompetitive BSEP inhibition for CP-724,714 and demonstrates that noncompetitive inhibition leads to much greater bile acid accumulation and potential toxicity. Our research demonstrates the potential for mechanistic modeling to contribute to the understanding of how bile acid transport inhibitors

Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science.

Science.gov (United States)

Cañete-Valdeón, José M; Wieringa, Roel; Smallbone, Kieran

2012-12-01

There is a growing interest in mathematical mechanistic modelling as a promising strategy for understanding tumour progression. This approach is accompanied by a methodological change of making research, in which models help to actively generate hypotheses instead of waiting for general principles to become apparent once sufficient data are accumulated. This paper applies recent research from philosophy of science to uncover three important problems of mechanistic modelling which may compromise its mainstream application, namely: the dilemma of formal and informal descriptions, the need to express degrees of confidence and the need of an argumentation framework. We report experience and research on similar problems from software engineering and provide evidence that the solutions adopted there can be transferred to the biological domain. We hope this paper can provoke new opportunities for further and profitable interdisciplinary research in the field.

Bird Migration Under Climate Change - A Mechanistic Approach Using Remote Sensing

Science.gov (United States)

Smith, James A.; Blattner, Tim; Messmer, Peter

2010-01-01

The broad-scale reductions and shifts that may be expected under climate change in the availability and quality of stopover habitat for long-distance migrants is an area of increasing concern for conservation biologists. Researchers generally have taken two broad approaches to the modeling of migration behaviour to understand the impact of these changes on migratory bird populations. These include models based on causal processes and their response to environmental stimulation, "mechanistic models", or models that primarily are based on observed animal distribution patterns and the correlation of these patterns with environmental variables, i.e. "data driven" models. Investigators have applied the latter technique to forecast changes in migration patterns with changes in the environment, for example, as might be expected under climate change, by forecasting how the underlying environmental data layers upon which the relationships are built will change over time. The learned geostatstical correlations are then applied to the modified data layers.. However, this is problematic. Even if the projections of how the underlying data layers will change are correct, it is not evident that the statistical relationships will remain the same, i.e. that the animal organism may not adapt its' behaviour to the changing conditions. Mechanistic models that explicitly take into account the physical, biological, and behaviour responses of an organism as well as the underlying changes in the landscape offer an alternative to address these shortcomings. The availability of satellite remote sensing observations at multiple spatial and temporal scales, coupled with advances in climate modeling and information technologies enable the application of the mechanistic models to predict how continental bird migration patterns may change in response to environmental change. In earlier work, we simulated the impact of effects of wetland loss and inter-annual variability on the fitness of

Global sensitivity analysis applied to drying models for one or a population of granules

DEFF Research Database (Denmark)

Mortier, Severine Therese F. C.; Gernaey, Krist; Thomas, De Beer

2014-01-01

The development of mechanistic models for pharmaceutical processes is of increasing importance due to a noticeable shift toward continuous production in the industry. Sensitivity analysis is a powerful tool during the model building process. A global sensitivity analysis (GSA), exploring sensitiv......The development of mechanistic models for pharmaceutical processes is of increasing importance due to a noticeable shift toward continuous production in the industry. Sensitivity analysis is a powerful tool during the model building process. A global sensitivity analysis (GSA), exploring...... sensitivity in a broad parameter space, is performed to detect the most sensitive factors in two models, that is, one for drying of a single granule and one for the drying of a population of granules [using population balance model (PBM)], which was extended by including the gas velocity as extra input...... compared to our earlier work. beta(2) was found to be the most important factor for the single particle model which is useful information when performing model calibration. For the PBM-model, the granule radius and gas temperature were found to be most sensitive. The former indicates that granulator...

Mechanistic modeling of heat transfer process governing pressure tube-to-calandria tube contact and fuel channel failure

International Nuclear Information System (INIS)

Luxat, J.C.

2002-01-01

Heat transfer behaviour and phenomena associated with ballooning deformation of a pressure tube into contact with a calandria tube have been analyzed and mechanistic models have been developed to describe the heat transfer and thermal-mechanical processes. These mechanistic models are applied to analyze experiments performed in various COG funded Contact Boiling Test series. Particular attention is given in the modeling to characterization of the conditions for which fuel channel failure may occur. Mechanistic models describing the governing heat transfer and thermal-mechanical processes are presented. The technical basis for characterizing parameters of the models from the general heat transfer literature is described. The validity of the models is demonstrated by comparison with experimental data. Fuel channel integrity criteria are proposed which are based upon three necessary and sequential mechanisms: Onset of CHF and local drypatch formation at contact; sustained film boiling in the post-contact period; and creep strain to failure of the calandria tube while in sustained film boiling. (author)

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

OpenAIRE

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S.; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M.; Tettelin, Herv?; White, Owen; Angiuoli, Samuel V.; Mahurkar, Anup; Fricke, W. Florian

2017-01-01

Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. Results CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. ...

Hidden Hydride Transfer as a Decisive Mechanistic Step in the Reactions of the Unligated Gold Carbide [AuC]+ with Methane under Ambient Conditions.

Science.gov (United States)

Li, Jilai; Zhou, Shaodong; Schlangen, Maria; Weiske, Thomas; Schwarz, Helmut

2016-10-10

The reactivity of the cationic gold carbide [AuC] + (bearing an electrophilic carbon atom) towards methane has been studied using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The product pairs generated, that is, Au + /C 2 H 4 , [Au(C 2 H 2 )] + /H 2 , and [C 2 H 3 ] + /AuH, point to the breaking and making of C-H, C-C, and H-H bonds under single-collision conditions. The mechanisms of these rather efficient reactions have been elucidated by high-level quantum-chemical calculations. As a major result, based on molecular orbital and NBO-based charge analysis, an unprecedented hydride transfer from methane to the carbon atom of [AuC] + has been identified as a key step. Also, the origin of this novel mechanistic scenario has been addressed. The mechanistic insights derived from this study may provide guidance for the rational design of carbon-based catalysts. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis

Energy Technology Data Exchange (ETDEWEB)

Casey, Charles P

2012-11-14

Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis Charles P. Casey, Principal Investigator Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706 Phone 608-262-0584 FAX: 608-262-7144 Email: casey@chem.wisc.edu http://www.chem.wisc.edu/main/people/faculty/casey.html Executive Summary. Our goal was to learn the intimate mechanistic details of reactions involved in homogeneous catalysis and to use the insight we gain to develop new and improved catalysts. Our work centered on the hydrogenation of polar functional groups such as aldehydes and ketones and on hydroformylation. Specifically, we concentrated on catalysts capable of simultaneously transferring hydride from a metal center and a proton from an acidic oxygen or nitrogen center to an aldehyde or ketone. An economical iron based catalyst was developed and patented. Better understanding of fundamental organometallic reactions and catalytic processes enabled design of energy and material efficient chemical processes. Our work contributed to the development of catalysts for the selective and mild hydrogenation of ketones and aldehydes; this will provide a modern green alternative to reductions by LiAlH4 and NaBH4, which require extensive work-up procedures and produce waste streams. (C5R4OH)Ru(CO)2H Hydrogenation Catalysts. Youval Shvo described a remarkable catalytic system in which the key intermediate (C5R4OH)Ru(CO)2H (1) has an electronically coupled acidic OH unit and a hydridic RuH unit. Our efforts centered on understanding and improving upon this important catalyst for reduction of aldehydes and ketones. Our mechanistic studies established that the reduction of aldehydes by 1 to produce alcohols and a diruthenium bridging hydride species occurs much more rapidly than regeneration of the ruthenium hydride from the diruthenium bridging hydride species. Our mechanistic studies require simultaneous transfer of hydride from ruthenium to

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

Science.gov (United States)

Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

2017-10-02

During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

Mechanistic Implications for the Ni(I-Catalyzed Kumada Cross-Coupling Reaction

Directory of Open Access Journals (Sweden)

Linda Iffland

2017-11-01

Full Text Available Herein we report on the cross-coupling reaction of phenylmagnesium bromide with aryl halides using the well-defined tetrahedral Ni(I complex, [(TriphosNiICl] (Triphos = 1,1,1-tris(diphenylphosphinomethylethane. In the presence of 0.5 mol % [(TriphosNiICl], good to excellent yields (75–97% of the respective coupling products within a reaction time of only 2.5 h at room temperature were achieved. Likewise, the tripodal Ni(IIcomplexes [(κ2-TriphosNiIICl2] and [(κ3-TriphosNiIICl](X (X = ClO4, BF4 were tested as potential pre-catalysts for the Kumada cross-coupling reaction. While the Ni(II complexes also afford the coupling products in comparable yields, mechanistic investigations by UV/Vis and electron paramagnetic resonance (EPR spectroscopy indicate a Ni(I intermediate as the catalytically active species in the Kumada cross-coupling reaction. Based on experimental findings and density functional theory (DFT calculations, a plausible Ni(I-catalyzed reaction mechanism for the Kumada cross-coupling reaction is presented.

Mechanistic Features of Nanodiamonds in the Lapping of Magnetic Heads

Directory of Open Access Journals (Sweden)

Xionghua Jiang

2014-01-01

Full Text Available Nanodiamonds, which are the main components of slurry in the precision lapping process of magnetic heads, play an important role in surface quality. This paper studies the mechanistic features of nanodiamond embedment into a Sn plate in the lapping process. This is the first study to develop mathematical models for nanodiamond embedment. Such models can predict the optimum parameters for particle embedment. From the modeling calculations, the embedded pressure satisfies p0=3/2·W/πa2 and the indentation depth satisfies δ=k1P/HV. Calculation results reveal that the largest embedded pressure is 731.48 GPa and the critical indentation depth δ is 7 nm. Atomic force microscopy (AFM, scanning electron microscopy (SEM, and Auger electron spectroscopy (AES were used to carry out surface quality detection and analysis of the disk head. Both the formation of black spots on the surface and the removal rate have an important correlation with the size of nanodiamonds. The results demonstrate that an improved removal rate (21 nm·min−1 can be obtained with 100 nm diamonds embedded in the plate.

Mechanistic features of nanodiamonds in the lapping of magnetic heads.

Science.gov (United States)

Jiang, Xionghua; Chen, Zhenxing; Wolfram, Joy; Yang, Zhizhou

2014-01-01

Nanodiamonds, which are the main components of slurry in the precision lapping process of magnetic heads, play an important role in surface quality. This paper studies the mechanistic features of nanodiamond embedment into a Sn plate in the lapping process. This is the first study to develop mathematical models for nanodiamond embedment. Such models can predict the optimum parameters for particle embedment. From the modeling calculations, the embedded pressure satisfies p 0 = (3/2) · (W/πa (2)) and the indentation depth satisfies δ = k1√P/HV. Calculation results reveal that the largest embedded pressure is 731.48 GPa and the critical indentation depth δ is 7 nm. Atomic force microscopy (AFM), scanning electron microscopy (SEM), and Auger electron spectroscopy (AES) were used to carry out surface quality detection and analysis of the disk head. Both the formation of black spots on the surface and the removal rate have an important correlation with the size of nanodiamonds. The results demonstrate that an improved removal rate (21 nm · min(-1)) can be obtained with 100 nm diamonds embedded in the plate.

Mechanistic modeling of CHF in forced-convection subcooled boiling

International Nuclear Information System (INIS)

Podowski, M.Z.; Alajbegovic, A.; Kurul, N.; Drew, D.A.; Lahey, R.T. Jr.

1997-05-01

Because of the complexity of phenomena governing boiling heat transfer, the approach to solve practical problems has traditionally been based on experimental correlations rather than mechanistic models. The recent progress in computational fluid dynamics (CFD), combined with improved experimental techniques in two-phase flow and heat transfer, makes the use of rigorous physically-based models a realistic alternative to the current simplistic phenomenological approach. The objective of this paper is to present a new CFD model for critical heat flux (CHF) in low quality (in particular, in subcooled boiling) forced-convection flows in heated channels

Corrigendum: Free Will and Punishment: A Mechanistic View of Human Nature Reduces Retribution.

Science.gov (United States)

2018-02-01

Original article: Shariff, A. F., Greene, J. D., Karremans, J. C., Luguri, J. B., Clark, C. J., Schooler, J. W., . . . Vohs, K. D. (2014). Free will and punishment: A mechanistic view of human nature reduces retribution. Psychological Science, 25, 1563-1570. doi:10.1177/0956797614534693.

Corrigendum: Free will and punishment: A mechanistic view of human nature reduces retribution

NARCIS (Netherlands)

Shariff, A.F.; Greene, J.D.; Karremans, J.C.T.M.; Luguri, J.B.; Clark, C.J.; Schooler, J.W.; Baumeister, R.F.; Vohs, K.D.

2018-01-01

Original article: Shariff, A. F., Greene, J. D., Karremans, J. C., Luguri, J. B., Clark, C. J., Schooler, J. W., . . . Vohs, K. D. (2014). Free will and punishment: A mechanistic view of human nature reduces retribution. Psychological Science, 25, 1563-1570. doi:10.1177/0956797614534693

A mechanistic model for electricity consumption on dairy farms: Definition, validation, and demonstration

NARCIS (Netherlands)

Upton, J.R.; Murphy, M.; Shallo, L.; Groot Koerkamp, P.W.G.; Boer, de I.J.M.

2014-01-01

Our objective was to define and demonstrate a mechanistic model that enables dairy farmers to explore the impact of a technical or managerial innovation on electricity consumption, associated CO2 emissions, and electricity costs. We, therefore, (1) defined a model for electricity consumption on

Comparative analysis of perturbed molecular pathways identified in in vitro and in vivo toxicology studies

NARCIS (Netherlands)

Wiesinger, Martin; Mayer, Bernd; Jennings, Paul; Lukas, Arno

The development of in vitro toxicological testing strategies are hampered by the difficulty in extrapolation to the intact organism. Academic toxicological literature contains a wealth of mechanistically rich information, especially arising from omic studies, which could potentially be utilized to

Mechanistic modeling of zircaloy deformation and fracture in fuel element analysis

International Nuclear Information System (INIS)

Nichols, F.A.

1987-01-01

A review is given of the comprehensive model developed in the 1960s at the Bettis Atomic Power Laboratory to explain the creep of Zircaloy during neutron irradiation and applied to fuel element analysis and design. The in-pile softening observed at low stresses was hypothesized to be due to a combination of the growth-directed Roberts-Cottrell yielding creep originally proposed for α-uranium and the formation of point defect loops preferentially on certain planes in response to the applied stress, with the second process being of relatively greater importance. The in-pile hardening observed at high stresses (or strain-rates) was proposed to be due to the cutting by dislocations of radiation-produced obstacles. In this stress (strain-rate) region, in-pile behavior was proposed to be identical to post-irradiation behavior. At intermediate stresses (strain-rates) a mechanism of radiation-enhanced climb around obstacles was suggested as being rate-controlling. As the stress is decreased, the climb process becomes easier, and the rate was then predicted to be controlled by glide at a flow-stress characteristic of unirradiated, annealed material, where radiation-enhanced diffusion enabled climbing around the normal strain-hardening obstacles. At still lower stresses, this glide process became negligibly slow compared with the growth-connected creep mechanism that was presumed to operate independently. The overall scheme was shown to be in good agreement with all the in-pile data then available and implemented into the computer analysis of fuel element behavior

Physiologically induced color-pattern changes in butterfly wings: mechanistic and evolutionary implications.

Science.gov (United States)

Otaki, Joji M

2008-07-01

A mechanistic understanding of the butterfly wing color-pattern determination can be facilitated by experimental pattern changes. Here I review physiologically induced color-pattern changes in nymphalid butterflies and their mechanistic and evolutionary implications. A type of color-pattern change can be elicited by elemental changes in size and position throughout the wing, as suggested by the nymphalid groundplan. These changes of pattern elements are bi-directional and bi-sided dislocation toward or away from eyespot foci and in both proximal and distal sides of the foci. The peripheral elements are dislocated even in the eyespot-less compartments. Anterior spots are more severely modified, suggesting the existence of an anterior-posterior gradient. In one species, eyespots are transformed into white spots with remnant-like orange scales, and such patterns emerge even at the eyespot-less "imaginary" foci. A series of these color-pattern modifications probably reveal "snap-shots" of a dynamic morphogenic signal due to heterochronic uncoupling between the signaling and reception steps. The conventional gradient model can be revised to account for these observed color-pattern changes.

Fidelity in Animal Modeling: Prerequisite for a Mechanistic Research Front Relevant to the Inflammatory Incompetence of Acute Pediatric Malnutrition

Science.gov (United States)

Woodward, Bill

2016-01-01

Inflammatory incompetence is characteristic of acute pediatric protein-energy malnutrition, but its underlying mechanisms remain obscure. Perhaps substantially because the research front lacks the driving force of a scholarly unifying hypothesis, it is adrift and research activity is declining. A body of animal-based research points to a unifying paradigm, the Tolerance Model, with some potential to offer coherence and a mechanistic impetus to the field. However, reasonable skepticism prevails regarding the relevance of animal models of acute pediatric malnutrition; consequently, the fundamental contributions of the animal-based component of this research front are largely overlooked. Design-related modifications to improve the relevance of animal modeling in this research front include, most notably, prioritizing essential features of pediatric malnutrition pathology rather than dietary minutiae specific to infants and children, selecting windows of experimental animal development that correspond to targeted stages of pediatric immunological ontogeny, and controlling for ontogeny-related confounders. In addition, important opportunities are presented by newer tools including the immunologically humanized mouse and outbred stocks exhibiting a magnitude of genetic heterogeneity comparable to that of human populations. Sound animal modeling is within our grasp to stimulate and support a mechanistic research front relevant to the immunological problems that accompany acute pediatric malnutrition. PMID:27077845

Fidelity in Animal Modeling: Prerequisite for a Mechanistic Research Front Relevant to the Inflammatory Incompetence of Acute Pediatric Malnutrition.

Science.gov (United States)

Woodward, Bill

2016-04-11

Inflammatory incompetence is characteristic of acute pediatric protein-energy malnutrition, but its underlying mechanisms remain obscure. Perhaps substantially because the research front lacks the driving force of a scholarly unifying hypothesis, it is adrift and research activity is declining. A body of animal-based research points to a unifying paradigm, the Tolerance Model, with some potential to offer coherence and a mechanistic impetus to the field. However, reasonable skepticism prevails regarding the relevance of animal models of acute pediatric malnutrition; consequently, the fundamental contributions of the animal-based component of this research front are largely overlooked. Design-related modifications to improve the relevance of animal modeling in this research front include, most notably, prioritizing essential features of pediatric malnutrition pathology rather than dietary minutiae specific to infants and children, selecting windows of experimental animal development that correspond to targeted stages of pediatric immunological ontogeny, and controlling for ontogeny-related confounders. In addition, important opportunities are presented by newer tools including the immunologically humanized mouse and outbred stocks exhibiting a magnitude of genetic heterogeneity comparable to that of human populations. Sound animal modeling is within our grasp to stimulate and support a mechanistic research front relevant to the immunological problems that accompany acute pediatric malnutrition.

Measuring populism: comparing two methods of content analysis

NARCIS (Netherlands)

Rooduijn, M.; Pauwels, T.

2011-01-01

The measurement of populism - particularly over time and space - has received only scarce attention. In this research note two different ways to measure populism are compared: a classical content analysis and a computer-based content analysis. An analysis of political parties in the United Kingdom,

In silico, experimental, mechanistic model for extended-release felodipine disposition exhibiting complex absorption and a highly variable food interaction.

Directory of Open Access Journals (Sweden)

Sean H J Kim

Full Text Available The objective of this study was to develop and explore new, in silico experimental methods for deciphering complex, highly variable absorption and food interaction pharmacokinetics observed for a modified-release drug product. Toward that aim, we constructed an executable software analog of study participants to whom product was administered orally. The analog is an object- and agent-oriented, discrete event system, which consists of grid spaces and event mechanisms that map abstractly to different physiological features and processes. Analog mechanisms were made sufficiently complicated to achieve prespecified similarity criteria. An equation-based gastrointestinal transit model with nonlinear mixed effects analysis provided a standard for comparison. Subject-specific parameterizations enabled each executed analog's plasma profile to mimic features of the corresponding six individual pairs of subject plasma profiles. All achieved prespecified, quantitative similarity criteria, and outperformed the gastrointestinal transit model estimations. We observed important subject-specific interactions within the simulation and mechanistic differences between the two models. We hypothesize that mechanisms, events, and their causes occurring during simulations had counterparts within the food interaction study: they are working, evolvable, concrete theories of dynamic interactions occurring within individual subjects. The approach presented provides new, experimental strategies for unraveling the mechanistic basis of complex pharmacological interactions and observed variability.

Diagnosing MOV problems using comparative trace analysis

International Nuclear Information System (INIS)

Leon, R.L.

1992-01-01

The paper presents the concept of comparative trace analysis and shows it to be very effective in diagnosing motor operated valve (MOV) problems. Comparative trace analysis is simply the process of interpreting simultaneously gathered traces, each presenting a different perspective on the same series of events. The opening and closing of a motor operated valve is such a series of events. The simultaneous traces are obtained using Liberty Technologies' Valve Operation Test and Evaluation System (VOTES)reg-sign. The traces include stem thrust, motor current, motor power factor, motor power, switch actuations, vibration in three different frequency bands, spring pack displacement, and spring pack force. Spare and auxiliary channels enable additional key parameters to be measured, such as differential pressure and stem displacement. Though not specifically illustrated in this paper, the VOTES system also provides for FFT analysis on all traces except switches

Predicting residential exposure to phthalate plasticizer emitted from vinyl flooring: a mechanistic analysis.

Science.gov (United States)

Xu, Ying; Hubal, Elaine A Cohen; Clausen, Per A; Little, John C

2009-04-01

A two-room model is developed to estimate the emission rate of di-2-ethylhexyl phthalate (DEHP) from vinyl flooring and the evolving gas-phase and adsorbed surface concentrations in a realistic indoor environment. Because the DEHP emission rate measured in a test chamber may be quite different from the emission rate from the same material in the indoor environment the model provides a convenient means to predict emissions and transport in a more realistic setting. Adsorption isotherms for phthalates and plasticizers on interior surfaces, such as carpet, wood, dust, and human skin, are derived from previous field and laboratory studies. Log-linear relationships between equilibrium parameters and chemical vapor pressure are obtained. The predicted indoor air DEHP concentration at steady state is 0.15 microg/m3. Room 1 reaches steady state within about one year, while the adjacent room reaches steady state about three months later. Ventilation rate has a strong influence on DEHP emission rate while total suspended particle concentration has a substantial impact on gas-phase concentration. Exposure to DEHP via inhalation, dermal absorption, and oral ingestion of dust is evaluated. The model clarifies the mechanisms that govern the release of DEHP from vinyl flooring and the subsequent interactions with interior surfaces, airborne particles, dust, and human skin. Although further model development, parameter identification, and model validation are needed, our preliminary model provides a mechanistic framework that elucidates exposure pathways for phthalate plasticizers, and can most likely be adapted to predict emissions and transport of other semivolatile organic compounds, such as brominated flame retardants and biocides, in a residential environment.

Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality.

Science.gov (United States)

Warnecke, Lisa; Turner, James M; Bollinger, Trent K; Misra, Vikram; Cryan, Paul M; Blehert, David S; Wibbelt, Gudrun; Willis, Craig K R

2013-08-23

White-nose syndrome is devastating North American bat populations but we lack basic information on disease mechanisms. Altered blood physiology owing to epidermal invasion by the fungal pathogen Geomyces destructans (Gd) has been hypothesized as a cause of disrupted torpor patterns of affected hibernating bats, leading to mortality. Here, we present data on blood electrolyte concentration, haematology and acid-base balance of hibernating little brown bats, Myotis lucifugus, following experimental inoculation with Gd. Compared with controls, infected bats showed electrolyte depletion (i.e. lower plasma sodium), changes in haematology (i.e. increased haematocrit and decreased glucose) and disrupted acid-base balance (i.e. lower CO2 partial pressure and bicarbonate). These findings indicate hypotonic dehydration, hypovolaemia and metabolic acidosis. We propose a mechanistic model linking tissue damage to altered homeostasis and morbidity/mortality.

Good Modeling Practice for PAT Applications: Propagation of Input Uncertainty and Sensitivity Analysis

DEFF Research Database (Denmark)

Sin, Gürkan; Gernaey, Krist; Eliasson Lantz, Anna

2009-01-01

The uncertainty and sensitivity analysis are evaluated for their usefulness as part of the model-building within Process Analytical Technology applications. A mechanistic model describing a batch cultivation of Streptomyces coelicolor for antibiotic production was used as case study. The input...... compared to the large uncertainty observed in the antibiotic and off-gas CO2 predictions. The output uncertainty was observed to be lower during the exponential growth phase, while higher in the stationary and death phases - meaning the model describes some periods better than others. To understand which...... promising for helping to build reliable mechanistic models and to interpret the model outputs properly. These tools make part of good modeling practice, which can contribute to successful PAT applications for increased process understanding, operation and control purposes. © 2009 American Institute...

A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

Science.gov (United States)

Suzuki, Tasuma

2009-01-01

Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics

Directory of Open Access Journals (Sweden)

Jaehee V. Shim

2017-09-01

Full Text Available Tyrosine kinase inhibitors (TKIs are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help to control critical processes such as survival signaling, energy homeostasis, and excitation–contraction coupling. However, mechanistic understanding is limited at present due to the complexities of tyrosine kinase signaling, and the wide range of targets inhibited by TKIs. Here, we review the use of TKIs in cancer and the cardiotoxicities that have been reported, discuss potential mechanisms underlying cardiotoxicity, and describe recent progress in achieving a more systematic understanding of cardiotoxicity via the use of mechanistic models. In particular, we argue that future advances are likely to be enabled by studies that combine large-scale experimental measurements with Quantitative Systems Pharmacology (QSP models describing biological mechanisms and dynamics. As such approaches have proven extremely valuable for understanding and predicting other drug toxicities, it is likely that QSP modeling can be successfully applied to cardiotoxicity induced by TKIs. We conclude by discussing a potential strategy for integrating genome-wide expression measurements with models, illustrate initial advances in applying this approach to cardiotoxicity, and describe challenges that must be overcome to truly develop a mechanistic and systematic understanding of cardiotoxicity caused by TKIs.

BANK RATING. A COMPARATIVE ANALYSIS

Directory of Open Access Journals (Sweden)

Batrancea Ioan

2015-07-01

Full Text Available Banks in Romania offers its customers a wide range of products but which involves both risk taking. Therefore researchers seek to build rating models to help managers of banks to risk of non-recovery of loans and interest. In the following we highlight rating Raiffeisen Bank, BCR-ERSTE Bank and Transilvania Bank, based on the models CAAMPL and Stickney making a comparative analysis of the two rating models.

Evolutionary and mechanistic drivers of laterality: A review and new synthesis.

Science.gov (United States)

Wiper, Mallory L

2017-11-01

Laterality, best understood as asymmetries of bilateral structures or biases in behaviour, has been demonstrated in species from all major vertebrate classes, and in many invertebrates, showing a large degree of evolutionary conservation across vertebrate groups. Despite the establishment of this phenomenon in so many species, however, the evolutionary and mechanistic study of laterality is uneven with numerous areas in this field requiring greater attention. Here, I present a partial review of how far the study of laterality has come, outlining previous pioneering work, I discuss the hypothesized costs and benefits of a lateralized brain and the suggested path of the evolution of laterality for populations and individuals. I propose an expansion of laterality research into areas that have been touched upon in the past but require stronger evidence from which the field will greatly benefit. Namely, I suggest a continuation of the phylogenetic approach to investigating laterality to better understand its evolutionary path; and a further focus on mechanistic drivers, with special attention to genetic and environmental effects. Putting together the puzzle of laterality using as many pieces as possible will provide a stronger understanding of this field, allowing us to continue to expand the field in novel ways.

Mechanistic variables can enhance predictive models of endotherm distributions: The American pika under current, past, and future climates

Science.gov (United States)

Mathewson, Paul; Moyer-Horner, Lucas; Beever, Erik; Briscoe, Natalie; Kearney, Michael T.; Yahn, Jeremiah; Porter, Warren P.

2017-01-01

How climate constrains species’ distributions through time and space is an important question in the context of conservation planning for climate change. Despite increasing awareness of the need to incorporate mechanism into species distribution models (SDMs), mechanistic modeling of endotherm distributions remains limited in this literature. Using the American pika (Ochotona princeps) as an example, we present a framework whereby mechanism can be incorporated into endotherm SDMs. Pika distribution has repeatedly been found to be constrained by warm temperatures, so we used Niche Mapper, a mechanistic heat-balance model, to convert macroclimate data to pika-specific surface activity time in summer across the western United States. We then explored the difference between using a macroclimate predictor (summer temperature) and using a mechanistic predictor (predicted surface activity time) in SDMs. Both approaches accurately predicted pika presences in current and past climate regimes. However, the activity models predicted 8–19% less habitat loss in response to annual temperature increases of ~3–5 °C predicted in the region by 2070, suggesting that pikas may be able to buffer some climate change effects through behavioral thermoregulation that can be captured by mechanistic modeling. Incorporating mechanism added value to the modeling by providing increased confidence in areas where different modeling approaches agreed and providing a range of outcomes in areas of disagreement. It also provided a more proximate variable relating animal distribution to climate, allowing investigations into how unique habitat characteristics and intraspecific phenotypic variation may allow pikas to exist in areas outside those predicted by generic SDMs. Only a small number of easily obtainable data are required to parameterize this mechanistic model for any endotherm, and its use can improve SDM predictions by explicitly modeling a widely applicable direct physiological effect

Mechanistic variables can enhance predictive models of endotherm distributions: the American pika under current, past, and future climates.

Science.gov (United States)

Mathewson, Paul D; Moyer-Horner, Lucas; Beever, Erik A; Briscoe, Natalie J; Kearney, Michael; Yahn, Jeremiah M; Porter, Warren P

2017-03-01

How climate constrains species' distributions through time and space is an important question in the context of conservation planning for climate change. Despite increasing awareness of the need to incorporate mechanism into species distribution models (SDMs), mechanistic modeling of endotherm distributions remains limited in this literature. Using the American pika (Ochotona princeps) as an example, we present a framework whereby mechanism can be incorporated into endotherm SDMs. Pika distribution has repeatedly been found to be constrained by warm temperatures, so we used Niche Mapper, a mechanistic heat-balance model, to convert macroclimate data to pika-specific surface activity time in summer across the western United States. We then explored the difference between using a macroclimate predictor (summer temperature) and using a mechanistic predictor (predicted surface activity time) in SDMs. Both approaches accurately predicted pika presences in current and past climate regimes. However, the activity models predicted 8-19% less habitat loss in response to annual temperature increases of ~3-5 °C predicted in the region by 2070, suggesting that pikas may be able to buffer some climate change effects through behavioral thermoregulation that can be captured by mechanistic modeling. Incorporating mechanism added value to the modeling by providing increased confidence in areas where different modeling approaches agreed and providing a range of outcomes in areas of disagreement. It also provided a more proximate variable relating animal distribution to climate, allowing investigations into how unique habitat characteristics and intraspecific phenotypic variation may allow pikas to exist in areas outside those predicted by generic SDMs. Only a small number of easily obtainable data are required to parameterize this mechanistic model for any endotherm, and its use can improve SDM predictions by explicitly modeling a widely applicable direct physiological effect

A MECHANISTIC STUDY OF RHODIUM TRI(ORTHO-TERT-BUTYLPHENYL)PHOSPHITE COMPLEXES AS HYDROFORMYLATION CATALYSTS

NARCIS (Netherlands)

JONGSMA, T; CHALLA, G; VANLEEUWEN, PWNM

1991-01-01

A mechanistic study of the hydroformylation cycle with a rhodium tri(o-t-butylphenyl)phosphite complex as catalyst is presented. Spectroscopic experiments prove that under hydroformylation conditions this complex is coordinated by only one phosphite. The complex has a high activity in the

National Launch System comparative economic analysis

Science.gov (United States)

Prince, A.

1992-01-01

Results are presented from an analysis of economic benefits (or losses), in the form of the life cycle cost savings, resulting from the development of the National Launch System (NLS) family of launch vehicles. The analysis was carried out by comparing various NLS-based architectures with the current Shuttle/Titan IV fleet. The basic methodology behind this NLS analysis was to develop a set of annual payload requirements for the Space Station Freedom and LEO, to design launch vehicle architectures around these requirements, and to perform life-cycle cost analyses on all of the architectures. A SEI requirement was included. Launch failure costs were estimated and combined with the relative reliability assumptions to measure the effects of losses. Based on the analysis, a Shuttle/NLS architecture evolving into a pressurized-logistics-carrier/NLS architecture appears to offer the best long-term cost benefit.

Comparative Genome Analysis of Enterobacter cloacae

Science.gov (United States)

Liu, Wing-Yee; Wong, Chi-Fat; Chung, Karl Ming-Kar; Jiang, Jing-Wei; Leung, Frederick Chi-Ching

2013-01-01

The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species. PMID:24069314

A Three-Stage Mechanistic Model for Solidification Cracking During Welding of Steel

Science.gov (United States)

Aucott, L.; Huang, D.; Dong, H. B.; Wen, S. W.; Marsden, J.; Rack, A.; Cocks, A. C. F.

2018-03-01

A three-stage mechanistic model for solidification cracking during TIG welding of steel is proposed from in situ synchrotron X-ray imaging of solidification cracking and subsequent analysis of fracture surfaces. Stage 1—Nucleation of inter-granular hot cracks: cracks nucleate inter-granularly in sub-surface where maximum volumetric strain is localized and volume fraction of liquid is less than 0.1; the crack nuclei occur at solute-enriched liquid pockets which remain trapped in increasingly impermeable semi-solid skeleton. Stage 2—Coalescence of cracks via inter-granular fracture: as the applied strain increases, cracks coalesce through inter-granular fracture; the coalescence path is preferential to the direction of the heat source and propagates through the grain boundaries to solidifying dendrites. Stage 3—Propagation through inter-dendritic hot tearing: inter-dendritic hot tearing occurs along the boundaries between solidifying columnar dendrites with higher liquid fraction. It is recommended that future solidification cracking criterion shall be based on the application of multiphase mechanics and fracture mechanics to the failure of semi-solid materials.

Polymerization kinetics of wheat gluten upon thermosetting. A mechanistic model.

Science.gov (United States)

Domenek, Sandra; Morel, Marie-Hélène; Bonicel, Joëlle; Guilbert, Stéphane

2002-10-09

Size exclusion high-performance liquid chromatography analysis was carried out on wheat gluten-glycerol blends subjected to different heat treatments. The elution profiles were analyzed in order to follow the solubility loss of protein fractions with specific molecular size. Owing to the known biochemical changes involved during the heat denaturation of gluten, a mechanistic mathematical model was developed, which divided the protein denaturation into two distinct reaction steps: (i) reversible change in protein conformation and (ii) protein precipitation through disulfide bonding between initially SDS-soluble and SDS-insoluble reaction partners. Activation energies of gluten unfolding, refolding, and precipitation were calculated with the Arrhenius law to 53.9 kJ x mol(-1), 29.5 kJ x mol(-1), and 172 kJ x mol(-1), respectively. The rate of protein solubility loss decreased as the cross-linking reaction proceeded, which may be attributed to the formation of a three-dimensional network progressively hindering the reaction. The enhanced susceptibility to aggregation of large molecules was assigned to a risen reaction probability due to their higher number of cysteine residues and to the increased percentage of unfolded and thereby activated proteins as complete protein refolding seemed to be an anticooperative process.

Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange.

Science.gov (United States)

Qiao, Liang; Cao, Minghao; Zheng, Jian; Zhao, Yihong; Zheng, Zhi-Liang

2017-10-30

The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). We reanalyzed the prior sweet orange fruit transcriptome data, leading to the identification of 72 genes highly correlated with the fruit sugar/acid ratio. The majority of these sugar/acid ratio-related genes are predicted to be involved in regulatory functions such as transport, signaling and transcription or encode enzymes involved in metabolism. Surprisingly, only three of these sugar/acid ratio-correlated genes are weakly correlated with sugar level and none of them overlaps with the acid-associated genes. Weighted Gene Coexpression Network Analysis (WGCNA) has revealed that these genes belong to four modules, Blue, Grey, Brown and Turquoise, with the former two modules being unique to the sugar/acid ratio control. Our results indicate that orange fruits contain a possible mechanistically distinct class of genes that may potentially be involved in maintaining fruit sugar/acid ratios and/or responding to the cellular sugar/acid ratio status. Therefore, our analysis of orange transcriptomes provides an intriguing insight into the potentially novel genetic or molecular mechanisms controlling the sugar/acid ratio in fruits.

Prediction of net hepatic release of glucose using a “hybrid” mechanistic model in ruminants applied to positive energy balance

OpenAIRE

Bahloul, Lahlou; Ortigues, Isabelle; Vernet, Jean; Lapierre, Helène; Noziere, Pierre; Sauvant, Daniel

2013-01-01

Ruminants depend on hepatic gluconeogenesis to meet most of their metabolic demand for glucose which relies on availability of precursors from diet supply and animal requirements (Loncke et al., 2010). Several mechanistic models of the metabolic fate of nutrients across the liver exist that have been parameterized for dairy cows. They cannot be directly used to predict hepatic gluconeogenesis in all types of ruminants in different physiological status. A hybrid mechanistic model of nutrient f...

Trichloroethylene: Mechanistic, epidemiologic and other supporting evidence of carcinogenic hazard.

Science.gov (United States)

Rusyn, Ivan; Chiu, Weihsueh A; Lash, Lawrence H; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z

2014-01-01

The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. The strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE. © 2013.

Combined In Situ Illumination-NMR-UV/Vis Spectroscopy: A New Mechanistic Tool in Photochemistry.

Science.gov (United States)

Seegerer, Andreas; Nitschke, Philipp; Gschwind, Ruth M

2018-06-18

Synthetic applications in photochemistry are booming. Despite great progress in the development of new reactions, mechanistic investigations are still challenging. Therefore, we present a fully automated in situ combination of NMR spectroscopy, UV/Vis spectroscopy, and illumination to allow simultaneous and time-resolved detection of paramagnetic and diamagnetic species. This optical fiber-based setup enables the first acquisition of combined UV/Vis and NMR spectra in photocatalysis, as demonstrated on a conPET process. Furthermore, the broad applicability of combined UVNMR spectroscopy for light-induced processes is demonstrated on a structural and quantitative analysis of a photoswitch, including rate modulation and stabilization of transient species by temperature variation. Owing to the flexibility regarding the NMR hardware, temperature, and light sources, we expect wide-ranging applications of this setup in various research fields. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

1991 comparative analysis of tritium in water

International Nuclear Information System (INIS)

Krause, W.J.; Mundschenk, H.

1992-06-01

For environmental monitoring of radioactive materials, the competent authorities of the States and Federal Government of Germany continuously perform measurements and make their results accessible to the public in an appropriate way. In order to guarantee the comparability of measured values and a high degree of reliability of the applied methods, the authorities in charge of carrying out such tasks are obliged to take part in the comparative analyses (ring tests) organized by the central offices of the Federal Government. Therefore, the aim of this comparative analysis performed by order of the Federal Ministry of the Environment, Nature Protection and Reactor Safety consists mainly in providing the measuring offices in charge of monitoring waters, with samples with known tritium contents in order to get an overview of the accuracy of currently used processes; check the accuracy of the determinations performed, and, if necessary, detect and eliminate systematic errors; check, in particular by means of the samples T2 and T3, the calibration of the measuring devices and, if necessary, make corrections. To this effect, the comparative analysis fulfills the function of quality control of the processes used in environmental monitoring. (orig./BBR) [de

Toxic neuropathies: Mechanistic insights based on a chemical perspective.

Science.gov (United States)

LoPachin, Richard M; Gavin, Terrence

2015-06-02

2,5-Hexanedione (HD) and acrylamide (ACR) are considered to be prototypical among chemical toxicants that cause central-peripheral axonopathies characterized by distal axon swelling and degeneration. Because the demise of distal regions was assumed to be causally related to the onset of neurotoxicity, substantial effort was devoted to deciphering the respective mechanisms. Continued research, however, revealed that expression of the presumed hallmark morphological features was dependent upon the daily rate of toxicant exposure. Indeed, many studies reported that the corresponding axonopathic changes were late developing effects that occurred independent of behavioral and/or functional neurotoxicity. This suggested that the toxic axonopathy classification might be based on epiphenomena related to dose-rate. Therefore, the goal of this mini-review is to discuss how quantitative morphometric analyses and the establishment of dose-dependent relationships helped distinguish primary, mechanistically relevant toxicant effects from non-specific consequences. Perhaps more importantly, we will discuss how knowledge of neurotoxicant chemical nature can guide molecular-level research toward a better, more rational understanding of mechanism. Our discussion will focus on HD, the neurotoxic γ-diketone metabolite of the industrial solvents n-hexane and methyl-n-butyl ketone. Early investigations suggested that HD caused giant neurofilamentous axonal swellings and eventual degeneration in CNS and PNS. However, as our review will point out, this interpretation underwent several iterations as the understanding of γ-diketone chemistry improved and more quantitative experimental approaches were implemented. The chemical concepts and design strategies discussed in this mini-review are broadly applicable to the mechanistic studies of other chemicals (e.g., n-propyl bromine, methyl methacrylate) that cause toxic neuropathies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A Mechanistic Model of Onset of Flow Instability Due to Mergence of Bubble Layers in a Vertical Narrow Rectangular Channel

Energy Technology Data Exchange (ETDEWEB)

Lee, Juh Yung; Chang, Soon Heung; Jeong, Yong [KAIST, Daejeon (Korea, Republic of)

2016-05-15

The onset of flow instability (OFI) is the one of important boiling phenomena since it may induce the premature critical heat flux (CHF) at the lowest heat flux level due to sudden flow excursion in a single channel of multichannel configuration. Especially prediction of OFI for narrow rectangular channel is very crucial in relevant to thermal-hydraulic design and safety analysis of open pool-type research reactors (RRs) using plate-type fuels. Based on high speed video (HSV) technique, the authors observed and determined that OFI and the minimum premature CHF in a narrow rectangular channel are induced by abrupt pressure drop fluctuation due to the mergence of facing bubble boundary layers (BLs) on opposite boiling surfaces. In this study, new mechanistic OFI model for narrow rectangular channel heated on both sides has been derived, which satisfies with the real triggering phenomena. Force balance approach was used for modeling of the maximum BLT since the quantity is comparable to the bubble departure diameter. From the validation with OFI database, it was shown that the new model fairly well predicts OFI heat flux for wide range of conditions.

Protection by caffeine against oxic radiation damage and chemical carcinogens : mechanistic considerations

International Nuclear Information System (INIS)

Kesavan, P.C.

1992-01-01

There is little doubt that caffeine administered after exposure to UV light enhances the damage to cells and organisms by inhibiting photoreactivation, excision and/or recombinational repair. However, when already present in the system, it affords remarkable protection not only against O 2 -dependent component of radiation damage, but also against chemical carcinogens that require metabolic activation. Possible mechanistic aspects are discussed briefly. (author). 81 refs

Mechanistic aspects of radioprotection by todralazine hydrochloride, a hematopoietic stem cell expanding agent

International Nuclear Information System (INIS)

Dimri, Manali; Joshi, Jaidev; Jain, Sanjoli; Ghosh, Subhajit; Srivastva, Nitisha; Prem Kumar, Indracanti; Chakrabarti, Rina

2014-01-01

Previously, we have reported todralazine hydrochloride, an antihypertensive drug, as a radioprotector and hematopoietic stem cell (HSC) expanding agent. The present study aims at unraveling mechanistic aspects of its radioprotective and HSC expanding potential. Zebrafish Tg (cmyb:GFP) embryos treated with 5 μM todralazine from 24-36 hours post fertilization (hpf), increased the number of HSCs (∼ 2 folds) at aorta gonad mesonephros (AGM) region. Similarly, the expression of HSC marker genes, runx1 (3.3 folds) and cMyb (1.4 folds) were also found to be increased. Further, todralazine also accelerated hematopoietic lineage production, erythropoiesis, as evaluated in chemical induced anemic model in zebrafish. Genome wide expression changes in todralazine treated embryos (from 24-36 hpf) using microarray, revealed up and down regulation of 645 and 429 genes respectively. Pathway analysis using DAVID database strongly suggested up regulation of wnt pathway (p<0.019253), which is known to involve in HSC expansion, in todralazine pre-treated embryos. NOS1, known to have its role in HSC expansion through wnt pathway, has been significantly upregulated (1.54 folds; q PCR) by todralazine treatment (from 24-36 hpf). Todralazine treatment (∼30 minutes; 20 Gy) led to a significant upregulation of antioxidant genes (SOD, catalase), DNA damage response genes (p53, p21, GADD45) and nucleotide excision repair genes (XPC, XPA, XPF, XPD) when compared to irradiated control. Immunohistochemical analysis of DNA damage marker (γH2AX) (30 minutes post irradiation), further supported radiation induced DNA damage and protection by todralazine pre-treatment. Corroborating these results, pre-irradiation treatment of todralazine reduced radiation induced apoptosis (caspase 3 assay). Overall, the results suggest that, todralazine protects zebrafish from radiation induced damages by upregulating antioxidant defense system, DNA damage recognition, DNA repair machinery and by reducing cell

Initial implementation of a comparative data analysis ontology.

Science.gov (United States)

Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

2009-07-03

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

Mechanistic aspects of the metal catalyzed alternating copolymerization of epoxides and carbon monoxide.

Science.gov (United States)

Allmendinger, Markus; Molnar, Ferenc; Zintl, Manuela; Luinstra, Gerrit A; Preishuber-Pflügl, Peter; Rieger, Bernhard

2005-09-05

The cobalt-catalyzed alternating copolymerization of epoxides and CO is a novel, direct approach to aliphatic polyesters, such as poly(hydroxybutyrate) (PHB). This reaction was found to be catalyzed by Ph3Si[Co(CO)4] (4) and pyridine affording in a first step the stable mono-insertion product Ph3Si-O-CH(CH3)-CH2-CO-Co(CO)4 (5). However, a profound mechanistic understanding, especially of the role of pyridine as the key component for the polymerization reaction was missing. ATR-IR online monitoring under catalytic conditions and DFT calculations were used to show that an acylpyridinium cation is formed by cleavage of the cobalt-acyl bond of 5 in the presence of pyridine. The Lewis acid thus generated activates the next incoming epoxide monomer for ring opening through [Co(CO)4]-. The catalytic cycle is completed by a subsequent CO insertion in the new cobalt-alkyl bond. The calculations are used to explore the energetic hypersurface of the polymerization reaction and are complemented by extended experimental investigations that also support the mechanistic hypotheses.

Mechanistic study of aerosol dry deposition on vegetated canopies

International Nuclear Information System (INIS)

Petroff, A.

2005-04-01

The dry deposition of aerosols onto vegetated canopies is modelled through a mechanistic approach. The interaction between aerosols and vegetation is first formulated by using a set of parameters, which are defined at the local scale of one surface. The overall deposition is then deduced at the canopy scale through an up-scaling procedure based on the statistic distribution parameters. This model takes into account the canopy structural and morphological properties, and the main characteristics of the turbulent flow. Deposition mechanisms considered are Brownian diffusion, interception, initial and turbulent impaction, initially with coniferous branches and then with entire canopies of different roughness, such as grass, crop field and forest. (author)

Mechanistic CHF modeling for natural circulation applications in SMR

Energy Technology Data Exchange (ETDEWEB)

Luitjens, Jeffrey [Department of Nuclear Engineering and Radiation Health Physics, Oregon State University, 3451 SW Jefferson Way, Corvallis, OR 97331 (United States); Wu, Qiao, E-mail: qiao.wu@oregonstate.edu [Department of Nuclear Engineering and Radiation Health Physics, Oregon State University, 3451 SW Jefferson Way, Corvallis, OR 97331 (United States); Greenwood, Scott; Corradini, Michael [Department of Engineering Physics, University of Wisconsin, 1415 Engineering Drive, Madison, WI 53706 (United States)

2016-12-15

A mechanistic critical heat flux correlation has been developed for a wide range of operating conditions which include low mass fluxes of 540–890 kg/m{sup 2}-s, high pressures of 12–13 MPa, and critical heat fluxes of 835–1100 kW/m{sup 2}. Eleven experimental data points have been collected over these conditions to inform the development of the model using bundle geometry. Errors of within 15% have been obtained with the proposed model for predicting the critical heat flux value, location, and critical pin power for a non-uniform heat flux applied to a 2 × 2 bundle configuration.

Heterogeneity of pulmonary perfusion as a mechanistic image-based phenotype in emphysema susceptible smokers.

Science.gov (United States)

Alford, Sara K; van Beek, Edwin J R; McLennan, Geoffrey; Hoffman, Eric A

2010-04-20

Recent evidence suggests that endothelial dysfunction and pathology of pulmonary vascular responses may serve as a precursor to smoking-associated emphysema. Although it is known that emphysematous destruction leads to vasculature changes, less is known about early regional vascular dysfunction which may contribute to and precede emphysematous changes. We sought to test the hypothesis, via multidetector row CT (MDCT) perfusion imaging, that smokers showing early signs of emphysema susceptibility have a greater heterogeneity in regional perfusion parameters than emphysema-free smokers and persons who had never smoked (NS). Assuming that all smokers have a consistent inflammatory response, increased perfusion heterogeneity in emphysema-susceptible smokers would be consistent with the notion that these subjects may have the inability to block hypoxic vasoconstriction in patchy, small regions of inflammation. Dynamic ECG-gated MDCT perfusion scans with a central bolus injection of contrast were acquired in 17 NS, 12 smokers with normal CT imaging studies (SNI), and 12 smokers with subtle CT findings of centrilobular emphysema (SCE). All subjects had normal spirometry. Quantitative image analysis determined regional perfusion parameters, pulmonary blood flow (PBF), and mean transit time (MTT). Mean and coefficient of variation were calculated, and statistical differences were assessed with one-way ANOVA. MDCT-based MTT and PBF measurements demonstrate globally increased heterogeneity in SCE subjects compared with NS and SNI subjects but demonstrate similarity between NS and SNI subjects. These findings demonstrate a functional lung-imaging measure that provides a more mechanistically oriented phenotype that differentiates smokers with and without evidence of emphysema susceptibility.

Validation of mechanistic models for gas precipitation in solids during postirradiation annealing experiments

Science.gov (United States)

Rest, J.

1989-12-01

A number of different phenomenological models for gas precipitation in solids during postirradiation annealing experiments have been proposed. Validation of such mechanistic models for gas release and swelling is complicated by the use of data containing large systematic errors, and phenomena characterized by synergistic effects as well as uncertainties in materials properties. Statistical regression analysis is recommended for the selection of a reasonably well characterized data base for gas release from irradiated fuel under transient heating conditions. It is demonstrated that an appropriate data selection method is required in order to realistically examine the impact of differing descriptions of the phenomena, and uncertainties in selected materials properties, on the validation results. The results of the analysis show that the kinetics of gas precipitation in solids depend on bubble overpressurization effects and need to be accounted for during the heatup phase of isothermal heating experiments. It is shown that if only the total gas release values (as opposed to time-dependent data) were available, differentiation between different gas precipitation models would be ambiguous. The observed sustained increase in the fractional release curve at relatively high temperatures after the total precipitation of intragranular gas in fission gas bubbles is ascribed to the effects of a grain-growth/grain-boundary sweeping mechanism.

Validation of mechanistic models for gas precipitation in solids during postirradiation annealing experiments

International Nuclear Information System (INIS)

Rest, J.

1989-01-01

A number of different phenomenological models for gas precipitation in solids during postirradiation annealing experiments have been proposed. Validation of such mechanistic models for gas release and swelling is complicated by the use of data containing large systematic errors, and phenomena characterized by synergistic effects as well as uncertainties in materials properties. Statistical regression analysis is recommended for the selection of a reasonably well characterized data base for gas release from irradiated fuel under transient heating conditions. It is demonstrated that an appropriate data selection method is required in order to realistically examine the impact of differing descriptions of the phenomena, and uncertainties in selected materials properties, on the validation results. The results of the analysis show that the kinetics of gas precipitation in solid depend on bubble overpressurization effects and need to be accounted for during the heatup phase of isothermal heating experiments. It is shown that if only the total gas release values (as opposed to time-dependent data) were available, differentiation between different gas precipitation models would be ambiguous. The observed sustained increase in the fractional release curve at relatively high temperatures after the total precipitation of intragranular gas in fission gas bubbles is ascribed to the effects of a grain-growth/grain-boundary sweeping mechanism. (orig.)

Mechanistic evidence for a ring-opening pathway in the Pd-catalyzed direct arylation of benzoxazoles

DEFF Research Database (Denmark)

Sanchez, R.S.; Zhuravlev, Fedor

2007-01-01

The direct Pd-catalyzed arylation of 5-substituted benzoxazoles, used as a mechanistic model for 1,3-azoles, was investigated experimentally and computationally. The results of the primary deuterium kinetic isotope effect, Hammett studies, and H/D exchange were shown to be inconsistent with the r......The direct Pd-catalyzed arylation of 5-substituted benzoxazoles, used as a mechanistic model for 1,3-azoles, was investigated experimentally and computationally. The results of the primary deuterium kinetic isotope effect, Hammett studies, and H/D exchange were shown to be inconsistent...... with the rate-limiting electrophilic or concerted palladation. A mechanism, proposed on the basis of kinetic and computational studies, includes generation of isocyanophenolate as the key step. The DFT calculations suggest that the overall catalytic cycle is facile and is largely controlled by the C-H acidity...

FOAM3D: A numerical simulator for mechanistic prediciton of foam displacement in multidimensions

Energy Technology Data Exchange (ETDEWEB)

Kovscek, A.R.; Patzek, T.W. [Lawrence Berkeley Laboratory, Berkeley, CA (United States); Radke, C.J. [Univ. of California, Berkeley, CA (United States)

1995-03-01

Field application of foam is a technically viable enhanced oil recovery process (EOR) as demonstrated by recent steam-foam field studies. Traditional gas-displacement processes, such as steam drive, are improved substantially by controlling gas mobility and thereby improving volumetric displacement efficiency. For instance, Patzek and Koinis showed major oil-recovery response after about two years of foam injection in two different pilot studies at the Kern River field. They report increased production of 5.5 to 14% of the original oil in place over a five year period. Because reservoir-scale simulation is a vital component of the engineering and economic evaluation of any EOR project, efficient application of foam as a displacement fluid requires a predictive numerical model of foam displacement. A mechanistic model would also expedite scale-up of the process from the laboratory to the field scale. No general, mechanistic, field-scale model for foam displacement is currently in use.

Mechanistic background and clinical applications of indocyanine green fluorescence imaging of hepatocellular carcinoma.

Science.gov (United States)

Ishizawa, Takeaki; Masuda, Koichi; Urano, Yasuteru; Kawaguchi, Yoshikuni; Satou, Shouichi; Kaneko, Junichi; Hasegawa, Kiyoshi; Shibahara, Junji; Fukayama, Masashi; Tsuji, Shingo; Midorikawa, Yutaka; Aburatani, Hiroyuki; Kokudo, Norihiro

2014-02-01

Although clinical applications of intraoperative fluorescence imaging of liver cancer using indocyanine green (ICG) have begun, the mechanistic background of ICG accumulation in the cancerous tissues remains unclear. In 170 patients with hepatocellular carcinoma cells (HCC), the liver surfaces and resected specimens were intraoperatively examined by using a near-infrared fluorescence imaging system after preoperative administration of ICG (0.5 mg/kg i.v.). Microscopic examinations, gene expression profile analysis, and immunohistochemical staining were performed for HCCs, which showed ICG fluorescence in the cancerous tissues (cancerous-type fluorescence), and HCCs showed fluorescence only in the surrounding non-cancerous liver parenchyma (rim-type fluorescence). ICG fluorescence imaging enabled identification of 273 of 276 (99%) HCCs in the resected specimens. HCCs showed that cancerous-type fluorescence was associated with higher cancer cell differentiation as compared with rim-type HCCs (P Fluorescence microscopy identified the presence of ICG in the canalicular side of the cancer cell cytoplasm, and pseudoglands of the HCCs showed a cancerous-type fluorescence pattern. The ratio of the gene and protein expression levels in the cancerous to non-cancerous tissues for Na(+)/taurocholate cotransporting polypeptide (NTCP) and organic anion-transporting polypeptide 8 (OATP8), which are associated with portal uptake of ICG by hepatocytes that tended to be higher in the HCCs that showed cancerous-type fluorescence than in those that showed rim-type fluorescence. Preserved portal uptake of ICG in differentiated HCC cells by NTCP and OATP8 with concomitant biliary excretion disorders causes accumulation of ICG in the cancerous tissues after preoperative intravenous administration. This enables highly sensitive identification of HCC by intraoperative ICG fluorescence imaging.

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

Science.gov (United States)

Pollard, Thomas D

2014-12-02

This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Comparative Analysis of 37 Acinetobacter Bacteriophages

Directory of Open Access Journals (Sweden)

Dann Turner

2017-12-01

Full Text Available Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.

Use of Gene Expression Changes in Blood to Elucidate Mechanistic Indicators of Childhood Asthma (MICA)

Science.gov (United States)

Risk assessment increasingly relies more heavily on mode of action, thus the identification of human bioindicators of disease becomes all the more important. Genomic methods represent a tool for both mode of action determination and bioindicator identification. The Mechanistic In...

comparative analysis of the compressive strength of hollow

African Journals Online (AJOL)

user

2016-04-02

Apr 2, 2016 ... Previous analysis showed that cavity size and number on one hand and combinations thickness affect the compressive strength of hollow sandcrete blocks. Series arrangement of the cavities is common but parallel arrangement has been recommended. This research performed a comparative analysis of ...

Initial Implementation of a comparative Data Analysis Ontology

Directory of Open Access Journals (Sweden)

Francisco Prosdocimi

2009-01-01

Full Text Available Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs, representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL, we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO. CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc. that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

Initial Implementation of a Comparative Data Analysis Ontology

Directory of Open Access Journals (Sweden)

Francisco Prosdocimi

2009-07-01

Full Text Available Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs, representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL, we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO. CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc. that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

Science.gov (United States)

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

2017-04-27

The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in genomics projects, while eliminating the need for on-site computational resources and expertise.

A 3-D CFD approach to the mechanistic prediction of forced convective critical heat flux at low quality

International Nuclear Information System (INIS)

Jean-Marie Le Corre; Cristina H Amon; Shi-Chune Yao

2005-01-01

Full text of publication follows: The prediction of the Critical Heat Flux (CHF) in a heat flux controlled boiling heat exchanger is important to assess the maximal thermal capability of the system. In the case of a nuclear reactor, CHF margin gain (using improved mixing vane grid design, for instance) can allow power up-rate and enhanced operating flexibility. In general, current nuclear core design procedures use quasi-1D approach to model the coolant thermal-hydraulic conditions within the fuel bundles coupled with fully empirical CHF prediction methods. In addition, several CHF mechanistic models have been developed in the past and coupled with 1D and quasi-1D thermal-hydraulic codes. These mechanistic models have demonstrated reasonable CHF prediction characteristics and, more remarkably, correct parametric trends over wide range of fluid conditions. However, since the phenomena leading to CHF are localized near the heater, models are needed to relate local quantities of interest to area-averaged quantities. As a consequence, large CHF prediction uncertainties may be introduced and 3D fluid characteristics (such as swirling flow) cannot be accounted properly. Therefore, a fully mechanistic approach to CHF prediction is, in general, not possible using the current approach. The development of CHF-enhanced fuel assembly designs requires the use of more advanced 3D coolant properties computations coupled with a CHF mechanistic modeling. In the present work, the commercial CFD code CFX-5 is used to compute 3D coolant conditions in a vertical heated tube with upward flow. Several CHF mechanistic models at low quality available in the literature are coupled with the CFD code by developing adequate models between local coolant properties and local parameters of interest to predict CHF. The prediction performances of these models are assessed using CHF databases available in the open literature and the 1995 CHF look-up table. Since CFD can reasonably capture 3D fluid

A mechanistic approach to the generation of sorption databases

International Nuclear Information System (INIS)

Bradbury, M.H.; Baeyens, B.

1992-01-01

Sorption of radionuclides in the near and far fields of an underground nuclear waste repository is one of the most important processes retarding their release to the environment. In the vast majority of cases sorption data have been presented in terms of empirical parameters such as distribution coefficients and isotherm equations. A consequence of this empirical methodology is that the sorption data are only strictly valid under the experimental conditions at which they were measured. Implicit in this approach is the need to generate large amounts of data and fitting parameters necessary for an empirical description of sorption under all realistically conceivable conditions which may arise in space and time along the migration pathway to Man. An alternative approach to the problem is to try to understand, and develop model descriptions of, underlying retention mechanisms and to identify those systems parameters which essentially determine the extent of sorption. The aim of this work is to see to what extent currently existing mechanistic models, together with their associated data, can be applied to predict sorption data from laboratory experiments on natural systems. This paper describes the current status of this work which is very much in an early stage of development. An example is given whereby model predictions are compared with laboratory results for the sorption of Np at trace concentrations under oxidizing conditions on a series of minerals relevant to granite formations. 31 refs., 11 figs., 5 tabs

rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

Science.gov (United States)

Ozer, Stuart; Doshi, Kishore J; Xu, Weijia; Gutell, Robin R

2011-12-31

Beyond its direct involvement in protein synthesis with mRNA, tRNA, and rRNA, RNA is now being appreciated for its significance in the overall metabolism and regulation of the cell. Comparative analysis has been very effective in the identification and characterization of RNA molecules, including the accurate prediction of their secondary structure. We are developing an integrative scalable data management and analysis system, the RNA Comparative Analysis Database (rCAD), implemented with SQL Server to support RNA comparative analysis. The platformagnostic database schema of rCAD captures the essential relationships between the different dimensions of information for RNA comparative analysis datasets. The rCAD implementation enables a variety of comparative analysis manipulations with multiple integrated data dimensions for advanced RNA comparative analysis workflows. In this paper, we describe details of the rCAD schema design and illustrate its usefulness with two usage scenarios.

Development of mechanistic sorption model and treatment of uncertainties for Ni sorption on montmorillonite/bentonite

International Nuclear Information System (INIS)

Ochs, Michael; Ganter, Charlotte; Tachi, Yukio; Suyama, Tadahiro; Yui, Mikazu

2011-02-01

Sorption and diffusion of radionuclides in buffer materials (bentonite) are the key processes in the safe geological disposal of radioactive waste, because migration of radionuclides in this barrier is expected to be diffusion-controlled and retarded by sorption processes. It is therefore necessary to understand the detailed/coupled processes of sorption and diffusion in compacted bentonite and develop mechanistic /predictive models, so that reliable parameters can be set under a variety of geochemical conditions relevant to performance assessment (PA). For this purpose, JAEA has developed the integrated sorption and diffusion (ISD) model/database in montmorillonite/bentonite systems. The main goal of the mechanistic model/database development is to provide a tool for a consistent explanation, prediction, and uncertainty assessment of K d as well as diffusion parameters needed for the quantification of radionuclide transport. The present report focuses on developing the thermodynamic sorption model (TSM) and on the quantification and handling of model uncertainties in applications, based on illustrating by example of Ni sorption on montmorillonite/bentonite. This includes 1) a summary of the present state of the art of thermodynamic sorption modeling, 2) a discussion of the selection of surface species and model design appropriate for the present purpose, 3) possible sources and representations of TSM uncertainties, and 4) details of modeling, testing and uncertainty evaluation for Ni sorption. Two fundamentally different approaches are presented and compared for representing TSM uncertainties: 1) TSM parameter uncertainties calculated by FITEQL optimization routines and some statistical procedure, 2) overall error estimated by direct comparison of modeled and experimental K d values. The overall error in K d is viewed as the best representation of model uncertainty in ISD model/database development. (author)

Combining Solvent Isotope Effects with Substrate Isotope Effects in Mechanistic Studies of Alcohol and Amine Oxidation by Enzymes*

Science.gov (United States)

Fitzpatrick, Paul F.

2014-01-01

Oxidation of alcohols and amines is catalyzed by multiple families of flavin-and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. PMID:25448013

An Emphasis on Perception: Teaching Image Formation Using a Mechanistic Model of Vision.

Science.gov (United States)

Allen, Sue; And Others

An effective way to teach the concept of image is to give students a model of human vision which incorporates a simple mechanism of depth perception. In this study two almost identical versions of a curriculum in geometrical optics were created. One used a mechanistic, interpretive eye model, and in the other the eye was modeled as a passive,…

From patterns to emerging processes in mechanistic urban ecology.

Science.gov (United States)

Shochat, Eyal; Warren, Paige S; Faeth, Stanley H; McIntyre, Nancy E; Hope, Diane

2006-04-01

Rapid urbanization has become an area of crucial concern in conservation owing to the radical changes in habitat structure and loss of species engendered by urban and suburban development. Here, we draw on recent mechanistic ecological studies to argue that, in addition to altered habitat structure, three major processes contribute to the patterns of reduced species diversity and elevated abundance of many species in urban environments. These activities, in turn, lead to changes in animal behavior, morphology and genetics, as well as in selection pressures on animals and plants. Thus, the key to understanding urban patterns is to balance studying processes at the individual level with an integrated examination of environmental forces at the ecosystem scale.

Mechanistic systems modeling to guide drug discovery and development.

Science.gov (United States)

Schmidt, Brian J; Papin, Jason A; Musante, Cynthia J

2013-02-01

A crucial question that must be addressed in the drug development process is whether the proposed therapeutic target will yield the desired effect in the clinical population. Pharmaceutical and biotechnology companies place a large investment on research and development, long before confirmatory data are available from human trials. Basic science has greatly expanded the computable knowledge of disease processes, both through the generation of large omics data sets and a compendium of studies assessing cellular and systemic responses to physiologic and pathophysiologic stimuli. Given inherent uncertainties in drug development, mechanistic systems models can better inform target selection and the decision process for advancing compounds through preclinical and clinical research. Copyright © 2012 Elsevier Ltd. All rights reserved.

Standardization: using comparative maintenance costs in an economic analysis

OpenAIRE

Clark, Roger Nelson

1987-01-01

Approved for public release; distribution is unlimited This thesis investigates the use of comparative maintenance costs of functionally interchangeable equipments in similar U.S. Navy shipboard applications in an economic analysis of standardization. The economics of standardization, life-cycle costing, and the Navy 3-M System are discussed in general. An analysis of 3-M System maintenance costs for a selected equipment, diesel engines, is conducted. The potential use of comparative ma...

Growth and lipid production of Umbelopsis isabellina on a solid substrate - Mechanistic modeling and validation

NARCIS (Netherlands)

Meeuwse, P.; Klok, A.J.; Haemers, S.; Tramper, J.; Rinzema, A.

2012-01-01

Microbial lipids are an interesting feedstock for biodiesel. Their production from agricultural waste streams by fungi cultivated in solid-state fermentation may be attractive, but the yield of this process is still quite low. In this article, a mechanistic model is presented that describes growth,

Mechanistic and kinetic aspects of pentose dehydration towards furfural in aqueous media employing homogeneous catalysis

NARCIS (Netherlands)

Danon, B.; Marcotullio, G.; De Jong, W.

2013-01-01

In this paper both the mechanistic and kinetic aspects of furfural formation from pentoses in aqueous acidic media have been reviewed. Based on the reviewed literature, a comprehensive reaction mechanism has been proposed consisting of more than one route, all starting from acyclic xylose, and

Arsenic Exposure and Type 2 Diabetes: MicroRNAs as Mechanistic Links?

OpenAIRE

Beck, Rowan; Styblo, Miroslav; Sethupathy, Praveen

2017-01-01

Purpose of Review The goal of this review is to delineate the following: (1) the primary means of inorganic arsenic (iAs) exposure for human populations, (2) the adverse public health outcomes associated with chronic iAs exposure, (3) the pathophysiological connection between arsenic and type 2 diabetes (T2D), and (4) the incipient evidence for microRNAs as candidate mechanistic links between iAs exposure and T2D. Recent Findings Exposure to iAs in animal models has been associated with the d...

A comparative integrated transcript analysis and functional characterization of differential mechanisms for induction of liver hypertrophy in the rat

International Nuclear Information System (INIS)

Boitier, Eric; Amberg, Alexander; Barbie, Valerie; Blichenberg, Arne; Brandenburg, Arnd; Gmuender, Hans; Gruhler, Albrecht; McCarthy, Diane; Meyer, Kirstin; Riefke, Bjoern; Raschke, Marian; Schoonen, Willem; Sieber, Maximilian; Suter, Laura; Thomas, Craig E.; Sajot, Nicolas

2011-01-01

The main goal of the present work was to better understand the molecular mechanisms underlying liver hypertrophy (LH), a recurrent finding observed following acute or repeated drug administration to animals, using transcriptomic technologies together with the results from conventional toxicology methods. Administration of 5 terminated proprietary drug candidates from participating companies involved in the EU Innomed PredTox Project or the reference hepatotoxicant troglitazone to rats for up to a 14-day duration induced LH as the main liver phenotypic toxicity outcome. The integrated analysis of transcriptomic liver expression data across studies turned out to be the most informative approach for the generation of mechanistic models of LH. In response to a xenobiotic stimulus, a marked increase in the expression of xenobiotic metabolizing enzymes (XME) was observed in a subset of 4 studies. Accumulation of these newly-synthesized proteins within the smooth endoplasmic reticulum (SER) would suggest proliferation of this organelle, which most likely is the main molecular process underlying the LH observed in XME studies. In another subset of 2 studies (including troglitazone), a marked up-regulation of genes involved in peroxisomal fatty acid β-oxidation was noted, associated with induction of genes involved in peroxisome proliferation. Therefore, an increase in peroxisome abundance would be the main mechanism underlying LH noted in this second study subset. Together, the use of transcript profiling provides a means to generate putative mechanistic models underlying the pathogenesis of liver hypertrophy, to distinguish between subtle variations in subcellular organelle proliferation and creates opportunities for improved mechanism-based risk assessment.

AIM analysis, synthetic, kinetic and mechanistic investigations of the ...

Indian Academy of Sciences (India)

analysis (NPA), atoms in molecules (AIM) methods and CHelpG keyword. ... obtained from studies of the effect of solvent, structure of reactions (different alkyl groups within the dialkyl ...... compounds) have provided useful evidence for steps 1.

Verification of the CONPAS (CONtainment Performance Analysis System) code package

International Nuclear Information System (INIS)

Kim, See Darl; Ahn, Kwang Il; Song, Yong Man; Choi, Young; Park, Soo Yong; Kim, Dong Ha; Jin, Young Ho.

1997-09-01

CONPAS is a computer code package to integrate the numerical, graphical, and results-oriented aspects of Level 2 probabilistic safety assessment (PSA) for nuclear power plants under a PC window environment automatically. For the integrated analysis of Level 2 PSA, the code utilizes four distinct, but closely related modules: (1) ET Editor, (2) Computer, (3) Text Editor, and (4) Mechanistic Code Plotter. Compared with other existing computer codes for Level 2 PSA, and CONPAS code provides several advanced features: computational aspects including systematic uncertainty analysis, importance analysis, sensitivity analysis and data interpretation, reporting aspects including tabling and graphic as well as user-friendly interface. The computational performance of CONPAS has been verified through a Level 2 PSA to a reference plant. The results of the CONPAS code was compared with an existing level 2 PSA code (NUCAP+) and the comparison proves that CONPAS is appropriate for Level 2 PSA. (author). 9 refs., 8 tabs., 14 figs

Mechanistic insights on the cycloisomerization of polyunsaturated precursors catalyzed by platinum and gold complexes.

Science.gov (United States)

Soriano, Elena; Marco-Contelles, José

2009-08-18

Organometallic chemistry provides powerful tools for the stereocontrolled synthesis of heterocycles and carbocycles. The electrophilic transition metals Pt(II) and Au(I, III) are efficient catalysts in these transitions and promote a variety of organic transformations of unsaturated precursors. These reactions produce functionalized cyclic and acyclic scaffolds for the synthesis of natural and non-natural products efficiently, under mild conditions, and with excellent chemoselectivity. Because these transformations are strongly substrate-dependent, they are versatile and may yield diverse molecular scaffolds. Therefore, synthetic chemists need a mechanistic interpretation to optimize this reaction process and design a new generation of catalysts. However, so far, no intermediate species has been isolated or characterized, so the formulated mechanistic hypotheses have been primarily based on labeling studies or trapping reactions. Recently, theoretical DFT studies have become a useful tool in our research, giving us insights into the key intermediates and into a variety of plausible reaction pathways. In this Account, we present a comprehensive mechanistic overview of transformations promoted by Pt and Au in a non-nucleophilic medium based on quantum-mechanical studies. The calculations are consistent with the experimental observations and provide fundamental insights into the versatility of these reaction processes. The reactivity of these metals results from their peculiar Lewis acid properties: the alkynophilic character of these soft metals and the pi-acid activation of unsaturated groups promotes the intra- or intermolecular attack of a nucleophile. 1,n-Enynes (n = 3-8) are particularly important precursors, and their transformation may yield a variety of cycloadducts depending on the molecular structure. However, the calculations suggest that these different cyclizations would have closely related reaction mechanisms, and we propose a unified mechanistic

Identify and Quantify the Mechanistic Sources of Sensor Performance Variation Between Individual Sensors SN1 and SN2

Energy Technology Data Exchange (ETDEWEB)

Diaz, Aaron A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baldwin, David L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cinson, Anthony D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Jones, Anthony M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Larche, Michael R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mathews, Royce [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mullen, Crystal A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Pardini, Allan F. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Posakony, Gerald J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Prowant, Matthew S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hartman, Trenton S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Edwards, Matthew K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-08-06

This Technical Letter Report satisfies the M3AR-14PN2301022 milestone, and is focused on identifying and quantifying the mechanistic sources of sensor performance variation between individual 22-element, linear phased-array sensor prototypes, SN1 and SN2. This effort constitutes an iterative evolution that supports the longer term goal of producing and demonstrating a pre-manufacturing prototype ultrasonic probe that possesses the fundamental performance characteristics necessary to enable the development of a high-temperature sodium-cooled fast reactor inspection system. The scope of the work for this portion of the PNNL effort conducted in FY14 includes performing a comparative evaluation and assessment of the performance characteristics of the SN1 and SN2 22 element PA-UT probes manufactured at PNNL. Key transducer performance parameters, such as sound field dimensions, resolution capabilities, frequency response, and bandwidth are used as a metric for the comparative evaluation and assessment of the SN1 and SN2 engineering test units.

Spatially confined photoinactivation of bacteria: towards novel tools for detailed mechanistic studies

Science.gov (United States)

Thomsen, Hanna; James, Jeemol; Farewell, Anne; Ericson, Marica B.

2018-02-01

Antimicrobial resistance is a serious global threat fueling an accelerated field of research aimed at developing novel antimicrobial therapies. A particular challenge is the treatment of microbial biofilms formed upon bacterial growth and often associated with chronic infections. Biofilms comprise bacteria that have adhered to a surface and formed 3D microcolonies, and demonstrate significantly increased antimicrobial resistance compared to the planktonic counterpart. A challenge in developing novel strategies for fighting these chronic infections is a lack of mechanistic understanding of what primarily contributes to enhanced drug resistance. Tools for noninvasive study of live biofilms are necessary to begin to understand these mechanisms on both a single cell and 3D level. Herein, a method by which multiphoton microscopy is implemented to study a biofilm model of Staphylococcus epidermidis to noninvasively visualize and measure penetration of compounds in 3D biofilm structure and two photon excitation was exploited for spatially confined photoinactivation and microscopy optimized for evaluation of microbiological viability at a microscopic level. Future studies are aimed at future development of the proposed techniques for detailed studies of, e.g., quorum sensing and mechanisms contributing to antimicrobial resistance.

Higher plant modelling for life support applications: first results of a simple mechanistic model

Science.gov (United States)

Hezard, Pauline; Dussap, Claude-Gilles; Sasidharan L, Swathy

2012-07-01

In the case of closed ecological life support systems, the air and water regeneration and food production are performed using microorganisms and higher plants. Wheat, rice, soybean, lettuce, tomato or other types of eatable annual plants produce fresh food while recycling CO2 into breathable oxygen. Additionally, they evaporate a large quantity of water, which can be condensed and used as potable water. This shows that recycling functions of air revitalization and food production are completely linked. Consequently, the control of a growth chamber for higher plant production has to be performed with efficient mechanistic models, in order to ensure a realistic prediction of plant behaviour, water and gas recycling whatever the environmental conditions. Purely mechanistic models of plant production in controlled environments are not available yet. This is the reason why new models must be developed and validated. This work concerns the design and test of a simplified version of a mathematical model coupling plant architecture and mass balance purposes in order to compare its results with available data of lettuce grown in closed and controlled chambers. The carbon exchange rate, water absorption and evaporation rate, biomass fresh weight as well as leaf surface are modelled and compared with available data. The model consists of four modules. The first one evaluates plant architecture, like total leaf surface, leaf area index and stem length data. The second one calculates the rate of matter and energy exchange depending on architectural and environmental data: light absorption in the canopy, CO2 uptake or release, water uptake and evapotranspiration. The third module evaluates which of the previous rates is limiting overall biomass growth; and the last one calculates biomass growth rate depending on matter exchange rates, using a global stoichiometric equation. All these rates are a set of differential equations, which are integrated with time in order to provide

Comparison of Two Mechanistic Microbial Growth Models to Estimate Shelf Life of Perishable Food Package under Dynamic Temperature Conditions

Directory of Open Access Journals (Sweden)

Dong Sun Lee

2014-01-01

Full Text Available Two mechanistic microbial growth models (Huang’s model and model of Baranyi and Roberts given in differential and integrated equation forms were compared in predicting the microbial growth and shelf life under dynamic temperature storage and distribution conditions. Literatures consistently reporting the microbial growth data under constant and changing temperature conditions were selected to obtain the primary model parameters, set up the secondary models, and apply them to predict the microbial growth and shelf life under fluctuating temperatures. When evaluated by general estimation behavior, bias factor, accuracy factor, and root-mean-square error, Huang’s model was comparable to Baranyi and Roberts’ model in the capability to estimate microbial growth under dynamic temperature conditions. Its simple form of single differential equation incorporating directly the growth rate and lag time may work as an advantage to be used in online shelf life estimation by using the electronic device.

SITE-94. Adaptation of mechanistic sorption models for performance assessment calculations

International Nuclear Information System (INIS)

Arthur, R.C.

1996-10-01

Sorption is considered in most predictive models of radionuclide transport in geologic systems. Most models simulate the effects of sorption in terms of empirical parameters, which however can be criticized because the data are only strictly valid under the experimental conditions at which they were measured. An alternative is to adopt a more mechanistic modeling framework based on recent advances in understanding the electrical properties of oxide mineral-water interfaces. It has recently been proposed that these 'surface-complexation' models may be directly applicable to natural systems. A possible approach for adapting mechanistic sorption models for use in performance assessments, using this 'surface-film' concept, is described in this report. Surface-acidity parameters in the Generalized Two-Layer surface complexation model are combined with surface-complexation constants for Np(V) sorption ob hydrous ferric oxide to derive an analytical model enabling direct calculation of corresponding intrinsic distribution coefficients as a function of pH, and Ca 2+ , Cl - , and HCO 3 - concentrations. The surface film concept is then used to calculate whole-rock distribution coefficients for Np(V) sorption by altered granitic rocks coexisting with a hypothetical, oxidized Aespoe groundwater. The calculated results suggest that the distribution coefficients for Np adsorption on these rocks could range from 10 to 100 ml/g. Independent estimates of K d for Np sorption in similar systems, based on an extensive review of experimental data, are consistent, though slightly conservative, with respect to the calculated values. 31 refs

Behavioural Procedural Models – a multipurpose mechanistic account

Directory of Open Access Journals (Sweden)

Leonardo Ivarola

2012-05-01

Full Text Available In this paper we outline an epistemological defence of what wecall Behavioural Procedural Models (BPMs, which represent the processes of individual decisions that lead to relevant economic patterns as psychologically (rather than rationally driven. Their general structure, and the way in which they may be incorporated to a multipurpose view of models, where the representational and interventionist goals are combined, is shown. It is argued that BPMs may provide “mechanistic-based explanations” in the sense defended by Hedström and Ylikoski (2010, which involve invariant regularities in Woodward’s sense. Such mechanisms provide a causal sort of explanation of anomalous economic patterns, which allow for extra marketintervention and manipulability in order to correct and improve some key individual decisions. This capability sets the basis for the so called libertarian paternalism (Sunstein and Thaler 2003.

Comparability of river suspended-sediment sampling and laboratory analysis methods

Science.gov (United States)

Groten, Joel T.; Johnson, Gregory D.

2018-03-06

Accurate measurements of suspended sediment, a leading water-quality impairment in many Minnesota rivers, are important for managing and protecting water resources; however, water-quality standards for suspended sediment in Minnesota are based on grab field sampling and total suspended solids (TSS) laboratory analysis methods that have underrepresented concentrations of suspended sediment in rivers compared to U.S. Geological Survey equal-width-increment or equal-discharge-increment (EWDI) field sampling and suspended sediment concentration (SSC) laboratory analysis methods. Because of this underrepresentation, the U.S. Geological Survey, in collaboration with the Minnesota Pollution Control Agency, collected concurrent grab and EWDI samples at eight sites to compare results obtained using different combinations of field sampling and laboratory analysis methods.Study results determined that grab field sampling and TSS laboratory analysis results were biased substantially low compared to EWDI sampling and SSC laboratory analysis results, respectively. Differences in both field sampling and laboratory analysis methods caused grab and TSS methods to be biased substantially low. The difference in laboratory analysis methods was slightly greater than field sampling methods.Sand-sized particles had a strong effect on the comparability of the field sampling and laboratory analysis methods. These results indicated that grab field sampling and TSS laboratory analysis methods fail to capture most of the sand being transported by the stream. The results indicate there is less of a difference among samples collected with grab field sampling and analyzed for TSS and concentration of fines in SSC. Even though differences are present, the presence of strong correlations between SSC and TSS concentrations provides the opportunity to develop site specific relations to address transport processes not captured by grab field sampling and TSS laboratory analysis methods.

The Cycloaddition of the Benzimidazolium Ylides with Alkynes: New Mechanistic Insights.

Directory of Open Access Journals (Sweden)

Costel Moldoveanu

Full Text Available New insights concerning the reaction mechanism in the cycloaddition reaction of benzimidazolium ylides to activated alkynes are presented. The proposed pathway leading both to 2-(1H-pyrrol-1-ylanilines and to pyrrolo[1,2-a]quinoxalin-4(5H-ones involves an opening of the imidazole ring from the cycloaddition product, followed by a nucleophilic attack of the aminic nitrogen to a proximal carbonyl group and the elimination of a leaving group. The mechanistic considerations are fully supported by experimental data, including the XRD resolved structure of the key reaction intermediate.

The Cycloaddition of the Benzimidazolium Ylides with Alkynes: New Mechanistic Insights.

Science.gov (United States)

Moldoveanu, Costel; Zbancioc, Gheorghita; Mantu, Dorina; Maftei, Dan; Mangalagiu, Ionel

2016-01-01

New insights concerning the reaction mechanism in the cycloaddition reaction of benzimidazolium ylides to activated alkynes are presented. The proposed pathway leading both to 2-(1H-pyrrol-1-yl)anilines and to pyrrolo[1,2-a]quinoxalin-4(5H)-ones involves an opening of the imidazole ring from the cycloaddition product, followed by a nucleophilic attack of the aminic nitrogen to a proximal carbonyl group and the elimination of a leaving group. The mechanistic considerations are fully supported by experimental data, including the XRD resolved structure of the key reaction intermediate.

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Science.gov (United States)

Tan, Shi Yang; Dutta, Avirup; Jakubovics, Nicholas S; Ang, Mia Yang; Siow, Cheuk Chuen; Mutha, Naresh Vr; Heydari, Hamed; Wee, Wei Yee; Wong, Guat Jah; Choo, Siew Woh

2015-01-16

Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the

Comparative Analysis of Terrorists’ Communication Strategies

Directory of Open Access Journals (Sweden)

Denis Alexandrovich Zhuravliev

2011-01-01

Full Text Available There is a wide-spread approach in a research literature to regard terrorism as a communicative process. From this point of view, the author offers a comparative analysis of the three most common communication strategies of terrorist groups, including transforming the role of the mass media, the Internet and a combined approach. The author also argues that a particular communication strategy determines a structure of a terrorist organization.

Mechanistic Prediction of the Effect of Microstructural Coarsening on Creep Response of SnAgCu Solder Joints

Science.gov (United States)

Mukherjee, S.; Chauhan, P.; Osterman, M.; Dasgupta, A.; Pecht, M.

2016-07-01

Mechanistic microstructural models have been developed to capture the effect of isothermal aging on time dependent viscoplastic response of Sn3.0Ag0.5Cu (SAC305) solders. SnAgCu (SAC) solders undergo continuous microstructural coarsening during both storage and service because of their high homologous temperature. The microstructures of these low melting point alloys continuously evolve during service. This results in evolution of creep properties of the joint over time, thereby influencing the long term reliability of microelectronic packages. It is well documented that isothermal aging degrades the creep resistance of SAC solder. SAC305 alloy is aged for (24-1000) h at (25-100)°C (~0.6-0.8 × T melt). Cross-sectioning and image processing techniques were used to periodically quantify the effect of isothermal aging on phase coarsening and evolution. The parameters monitored during isothermal aging include size, area fraction, and inter-particle spacing of nanoscale Ag3Sn intermetallic compounds (IMCs) and the volume fraction of micronscale Cu6Sn5 IMCs, as well as the area fraction of pure tin dendrites. Effects of microstructural evolution on secondary creep constitutive response of SAC305 solder joints were then modeled using a mechanistic multiscale creep model. The mechanistic phenomena modeled include: (1) dispersion strengthening by coarsened nanoscale Ag3Sn IMCs in the eutectic phase; and (2) load sharing between pro-eutectic Sn dendrites and the surrounding coarsened eutectic Sn-Ag phase and microscale Cu6Sn5 IMCs. The coarse-grained polycrystalline Sn microstructure in SAC305 solder was not captured in the above model because isothermal aging does not cause any significant change in the initial grain size and orientation of SAC305 solder joints. The above mechanistic model can successfully capture the drop in creep resistance due to the influence of isothermal aging on SAC305 single crystals. Contribution of grain boundary sliding to the creep strain of

A mechanistic model of an upper bound on oceanic carbon export as a function of mixed layer depth and temperature

Directory of Open Access Journals (Sweden)

Z. Li

2017-11-01

Full Text Available Export production reflects the amount of organic matter transferred from the ocean surface to depth through biological processes. This export is in large part controlled by nutrient and light availability, which are conditioned by mixed layer depth (MLD. In this study, building on Sverdrup's critical depth hypothesis, we derive a mechanistic model of an upper bound on carbon export based on the metabolic balance between photosynthesis and respiration as a function of MLD and temperature. We find that the upper bound is a positively skewed bell-shaped function of MLD. Specifically, the upper bound increases with deepening mixed layers down to a critical depth, beyond which a long tail of decreasing carbon export is associated with increasing heterotrophic activity and decreasing light availability. We also show that in cold regions the upper bound on carbon export decreases with increasing temperature when mixed layers are deep, but increases with temperature when mixed layers are shallow. A meta-analysis shows that our model envelopes field estimates of carbon export from the mixed layer. When compared to satellite export production estimates, our model indicates that export production in some regions of the Southern Ocean, particularly the subantarctic zone, is likely limited by light for a significant portion of the growing season.

Inferring spatial memory and spatiotemporal scaling from GPS data: comparing red deer Cervus elaphus movements with simulation models.

Science.gov (United States)

Gautestad, Arild O; Loe, Leif E; Mysterud, Atle

2013-05-01

1. Increased inference regarding underlying behavioural mechanisms of animal movement can be achieved by comparing GPS data with statistical mechanical movement models such as random walk and Lévy walk with known underlying behaviour and statistical properties. 2. GPS data are typically collected with ≥ 1 h intervals not exactly tracking every mechanistic step along the movement path, so a statistical mechanical model approach rather than a mechanistic approach is appropriate. However, comparisons require a coherent framework involving both scaling and memory aspects of the underlying process. Thus, simulation models have recently been extended to include memory-guided returns to previously visited patches, that is, site fidelity. 3. We define four main classes of movement, differing in incorporation of memory and scaling (based on respective intervals of the statistical fractal dimension D and presence/absence of site fidelity). Using three statistical protocols to estimate D and site fidelity, we compare these main movement classes with patterns observed in GPS data from 52 females of red deer (Cervus elaphus). 4. The results show best compliance with a scale-free and memory-enhanced kind of space use; that is, a power law distribution of step lengths, a fractal distribution of the spatial scatter of fixes and site fidelity. 5. Our study thus demonstrates how inference regarding memory effects and a hierarchical pattern of space use can be derived from analysis of GPS data. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Comparative Analysis of the Effects of Organization Development ...

African Journals Online (AJOL)

Comparative Analysis of the Effects of Organization Development Interventions on Organizational Leadership and Management Practice: A Case Of Green Earth Program (GEP) ... Journal of Language, Technology & Entrepreneurship in Africa.

Coupling machine learning with mechanistic models to study runoff production and river flow at the hillslope scale

Science.gov (United States)

Marçais, J.; Gupta, H. V.; De Dreuzy, J. R.; Troch, P. A. A.

2016-12-01

Geomorphological structure and geological heterogeneity of hillslopes are major controls on runoff responses. The diversity of hillslopes (morphological shapes and geological structures) on one hand, and the highly non linear runoff mechanism response on the other hand, make it difficult to transpose what has been learnt at one specific hillslope to another. Therefore, making reliable predictions on runoff appearance or river flow for a given hillslope is a challenge. Applying a classic model calibration (based on inverse problems technique) requires doing it for each specific hillslope and having some data available for calibration. When applied to thousands of cases it cannot always be promoted. Here we propose a novel modeling framework based on coupling process based models with data based approach. First we develop a mechanistic model, based on hillslope storage Boussinesq equations (Troch et al. 2003), able to model non linear runoff responses to rainfall at the hillslope scale. Second we set up a model database, representing thousands of non calibrated simulations. These simulations investigate different hillslope shapes (real ones obtained by analyzing 5m digital elevation model of Brittany and synthetic ones), different hillslope geological structures (i.e. different parametrizations) and different hydrologic forcing terms (i.e. different infiltration chronicles). Then, we use this model library to train a machine learning model on this physically based database. Machine learning model performance is then assessed by a classic validating phase (testing it on new hillslopes and comparing machine learning with mechanistic outputs). Finally we use this machine learning model to learn what are the hillslope properties controlling runoffs. This methodology will be further tested combining synthetic datasets with real ones.

Development Of The Computer Code For Comparative Neutron Activation Analysis

International Nuclear Information System (INIS)

Purwadi, Mohammad Dhandhang

2001-01-01

The qualitative and quantitative chemical analysis with Neutron Activation Analysis (NAA) is an importance utilization of a nuclear research reactor, and this should be accelerated and promoted in application and its development to raise the utilization of the reactor. The application of Comparative NAA technique in GA Siwabessy Multi Purpose Reactor (RSG-GAS) needs special (not commercially available yet) soft wares for analyzing the spectrum of multiple elements in the analysis at once. The application carried out using a single spectrum software analyzer, and comparing each result manually. This method really degrades the quality of the analysis significantly. To solve the problem, a computer code was designed and developed for comparative NAA. Spectrum analysis in the code is carried out using a non-linear fitting method. Before the spectrum analyzed, it was passed to the numerical filter which improves the signal to noise ratio to do the deconvolution operation. The software was developed using the G language and named as PASAN-K The testing result of the developed software was benchmark with the IAEA spectrum and well operated with less than 10 % deviation

Comparative risk analysis for the Rocky Flats Plant integrated project planning

International Nuclear Information System (INIS)

Jones, M.E.; Shain, D.I.

1994-01-01

The Rocky Flats Plant is developing, with active stakeholder participation, a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs, relative risks to workers and the public, and waste disposition are all needed. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risks from postulated options or endstates and is an analytical tool for the Rocky Flats Plant Integrated Project Planning which can assist a decision-maker in evaluating relative risks among proposed remediation activity. However, risks from all of the remediation activities, decontamination and decommissioning activities, and normal ongoing operations are imposed upon the Rocky Flats workers, the surrounding public, and the environment. Comparative Risk Analysis will provide risk information, both human health and ecological, to aid in reducing unnecessary resource and monetary expenditures by focusing these resources on the largest risks first. Comparative Risk Analysis has been developed to aggregate various incremental risk estimates to develop a site cumulative risk estimate. The Comparative Risk Analysis methodology Group, consisting of community stakeholders, was established. Early stakeholder involvement in the risk analysis methodology development provides an opportunity for stakeholders to influence the risk information delivered to a decision-maker. This paper discusses development of the Comparative Risk Analysis methodology, stakeholder participation and lessons learned from these challenges

Mechanistic assessment of hillslope transpiration controls of diel subsurface flow: a steady-state irrigation approach

Science.gov (United States)

H.R. Barnard; C.B. Graham; W.J. van Verseveld; J.R. Brooks; B.J. Bond; J.J. McDonnell

2010-01-01

Mechanistic assessment of how transpiration influences subsurface flow is necessary to advance understanding of catchment hydrology. We conducted a 24-day, steady-state irrigation experiment to quantify the relationships among soil moisture, transpiration and hillslope subsurface flow. Our objectives were to: (1) examine the time lag between maximum transpiration and...

How phenyl makes a difference: mechanistic insights into the ruthenium( ii )-catalysed isomerisation of allylic alcohols

KAUST Repository

Manzini, Simone

2013-10-16

[RuCl(η5-3-phenylindenyl)(PPh3)2] (1) has been shown to be a highly active catalyst for the isomerisation of allylic alcohols to the corresponding ketones. A variety of substrates undergo the transformation, typically with 0.25-0.5 mol% of catalyst at room temperature, outperforming commonly-used complexes such as [RuCl(Cp)(PPh3) 2] and [RuCl(η5-indenyl)(PPh3) 2]. Mechanistic experiments and density functional theory have been employed to investigate the mechanism and understand the effect of catalyst structure on reactivity. These investigations suggest a oxo-π-allyl mechanism is in operation, avoiding intermediate ruthenium hydride complexes and leading to a characteristic 1,3-deuterium shift. Important mechanistic insights from DFT and experiments also allowed for the design of a protocol that expands the scope of the transformation to include primary allylic alcohols. © 2013 The Royal Society of Chemistry.

How phenyl makes a difference: mechanistic insights into the ruthenium( ii )-catalysed isomerisation of allylic alcohols

KAUST Repository

Manzini, Simone; Poater, Albert; Nelson, David J.; Cavallo, Luigi; Nolan, Steven P.

2013-01-01

[RuCl(η5-3-phenylindenyl)(PPh3)2] (1) has been shown to be a highly active catalyst for the isomerisation of allylic alcohols to the corresponding ketones. A variety of substrates undergo the transformation, typically with 0.25-0.5 mol% of catalyst at room temperature, outperforming commonly-used complexes such as [RuCl(Cp)(PPh3) 2] and [RuCl(η5-indenyl)(PPh3) 2]. Mechanistic experiments and density functional theory have been employed to investigate the mechanism and understand the effect of catalyst structure on reactivity. These investigations suggest a oxo-π-allyl mechanism is in operation, avoiding intermediate ruthenium hydride complexes and leading to a characteristic 1,3-deuterium shift. Important mechanistic insights from DFT and experiments also allowed for the design of a protocol that expands the scope of the transformation to include primary allylic alcohols. © 2013 The Royal Society of Chemistry.

Comparative Analysis of the Main Business Intelligence Solutions

OpenAIRE

Alexandra RUSANEANU

2013-01-01

Nowadays, Business Intelligence solutions are the main tools for analyzing and monitoring the company’s performance at any organizational level. This paper presents a comparative analysis of the most powerful Business Intelligence solutions using a set of technical features such as infrastructure of the platform, development facilities, complex analysis tools, interactive dashboards and scorecards, mobile integration and complex implementation of performance management methodologies.

Establishing appropriate inputs when using the mechanistic-empirical pavement design guide to design rigid pavements in Pennsylvania.

Science.gov (United States)

2011-03-01

Each design input in the Mechanistic-Empirical Design Guide (MEPDG) required for the design of Jointed Plain Concrete : Pavements (JPCPs) is introduced and discussed in this report. Best values for Pennsylvania conditions were established and : recom...

Genome-wide comparative analysis of four Indian Drosophila species.

Science.gov (United States)

Mohanty, Sujata; Khanna, Radhika

2017-12-01

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

A mechanistic model for the evolution of multicellularity

Science.gov (United States)

Amado, André; Batista, Carlos; Campos, Paulo R. A.

2018-02-01

Through a mechanistic approach we investigate the formation of aggregates of variable sizes, accounting mechanisms of aggregation, dissociation, death and reproduction. In our model, cells can produce two metabolites, but the simultaneous production of both metabolites is costly in terms of fitness. Thus, the formation of larger groups can favor the aggregates to evolve to a configuration where division of labor arises. It is assumed that the states of the cells in a group are those that maximize organismal fitness. In the model it is considered that the groups can grow linearly, forming a chain, or compactly keeping a roughly spherical shape. Starting from a population consisting of single-celled organisms, we observe the formation of groups with variable sizes and usually much larger than two-cell aggregates. Natural selection can favor the formation of large groups, which allows the system to achieve new and larger fitness maxima.

Comparative Economic Analysis of Beekeeping Using Traditional ...

African Journals Online (AJOL)

The study was carried out in Tabora and Katavi regions in the miombo woodlands of Tanzania. The overall objective of the study was to undertake a comparative economic analysis of beekeeping using improved or traditional beehives. Data were collected from 198 beekeepers that were randomly selected from a sampling ...

Application of response surface methodology and semi-mechanistic model to optimize fluoride removal using crushed concrete in a fixed-bed column.

Science.gov (United States)

Gu, Bon-Wun; Lee, Chang-Gu; Park, Seong-Jik

2018-03-01

The aim of this study was to investigate the removal of fluoride from aqueous solutions by using crushed concrete fines as a filter medium under varying conditions of pH 3-7, flow rate of 0.3-0.7 mL/min, and filter depth of 10-20 cm. The performance of fixed-bed columns was evaluated on the basis of the removal ratio (Re), uptake capacity (qe), degree of sorbent used (DoSU), and sorbent usage rate (SUR) obtained from breakthrough curves (BTCs). Three widely used semi-mechanistic models, that is, Bohart-Adams, Thomas, and Yoon-Nelson models, were applied to simulate the BTCs and to derive the design parameters. The Box-Behnken design of response surface methodology (RSM) was used to elucidate the individual and interactive effects of the three operational parameters on the column performance and to optimize these parameters. The results demonstrated that pH is the most important factor in the performance of fluoride removal by a fixed-bed column. The flow rate had a significant negative influence on Re and DoSU, and the effect of filter depth was observed only in the regression model for DoSU. Statistical analysis indicated that the model attained from the RSM study is suitable for describing the semi-mechanistic model parameters.

Simulating the Risk of Liver Fluke Infection using a Mechanistic Hydro-epidemiological Model

Science.gov (United States)

Beltrame, Ludovica; Dunne, Toby; Rose, Hannah; Walker, Josephine; Morgan, Eric; Vickerman, Peter; Wagener, Thorsten

2016-04-01

Liver Fluke (Fasciola hepatica) is a common parasite found in livestock and responsible for considerable economic losses throughout the world. Risk of infection is strongly influenced by climatic and hydrological conditions, which characterise the host environment for parasite development and transmission. Despite on-going control efforts, increases in fluke outbreaks have been reported in recent years in the UK, and have been often attributed to climate change. Currently used fluke risk models are based on empirical relationships derived between historical climate and incidence data. However, hydro-climate conditions are becoming increasingly non-stationary due to climate change and direct anthropogenic impacts such as land use change, making empirical models unsuitable for simulating future risk. In this study we introduce a mechanistic hydro-epidemiological model for Liver Fluke, which explicitly simulates habitat suitability for disease development in space and time, representing the parasite life cycle in connection with key environmental conditions. The model is used to assess patterns of Liver Fluke risk for two catchments in the UK under current and potential future climate conditions. Comparisons are made with a widely used empirical model employing different datasets, including data from regional veterinary laboratories. Results suggest that mechanistic models can achieve adequate predictive ability and support adaptive fluke control strategies under climate change scenarios.

A tissue-engineered gastric cancer model for mechanistic study of anti-tumor drugs

International Nuclear Information System (INIS)

Gao, Ming; Cai, Yiting; Wu, Wei; Shi, Yazhou; Fei, Zhewei

2013-01-01

The use of the traditional xenograft subcutaneous tumor model has been contested because of its limitations, such as a slow tumorigenesis, inconsistent chemotherapeutic results, etc. In light of these challenges, we aim to revamp the traditional model by employing an electrospun scaffold composed of polydioxanone, gelatin and elastin to boost the tumorigenesis. The scaffold featured a highly porous microstructure and successfully supported the growth of tumor cells in vitro without provoking apoptosis. In vivo studies showed that in the scaffold model the tumor volume increased by 43.27% and the weight by 75.58%, respectively, within a 12-week period. In addition, the scaffold model saw an increase of CD24 + and CD44 + cells in the tumor mass by 42% and 313%, respectively. The scaffolding materials did not lead to phenotypic changes during the tumorigenesis. Thereafter, in the scaffold model, we found that the chemotherapeutic regimen of docetaxel, cisplatin and fluorouracil unleashed a stronger capability than the regimen comprising cisplatin and fluorouracil to deplete the CD44 + subpopulation. This discovery sheds mechanistic lights on the role of docetaxel for its future chemotherapeutic applications. This revamped model affords cancer scientists a convenient and reliable platform to mechanistically investigate the chemotherapeutic drugs on gastric cancer stem cells. (paper)

On the antibacterial effects of manuka honey: mechanistic insights

Directory of Open Access Journals (Sweden)

Roberts AEL

2015-10-01

Full Text Available Aled Edward Lloyd Roberts,* Helen Louise Brown,* Rowena Eleri Jenkins Department of Biomedical Sciences, Cardiff Metropolitan University, Cardiff, Wales, UK *These authors contributed equally to this work Abstract: Antimicrobial resistance (AMR is an increasing clinical problem precipitated by the inappropriate use of antibiotics in the later parts of the 20th Century. This problem, coupled with the lack of novel therapeutics in the development pipeline, means AMR is reaching crisis point, with an expected annual death rate of ten million people worldwide by 2050. To reduce, and to potentially remedy this problem, many researchers are looking into natural compounds with antimicrobial and/or antivirulence activity. Manuka honey is an ancient antimicrobial remedy with a good track record against a wide range of nosocomial pathogens that have increased AMR. Its inhibitory effects are the result of its constituent components, which add varying degrees of antimicrobial efficacy to the overall activity of manuka honey. The antimicrobial efficacy of manuka honey and some of its constituent components (such as methylglyoxal and leptosperin are known to bestow some degree of antimicrobial efficacy to manuka honey. Despite growing in vitro evidence of its antimicrobial efficacy, the in vivo use of manuka honey (especially in a clinical environment has been unexpectedly slow, partly due to the lack of mechanistic data. The mechanism by which manuka honey achieves its inhibitory efficacy has recently been identified against Staphylococcus aureus and Pseudomonas aeruginosa, with both of these contrasting organisms being inhibited through different mechanisms. Manuka honey inhibits S. aureus by interfering with the cell division process, whereas P. aeruginosa cells lyse in its presence due to the reduction of a key structural protein. In addition to these inhibitory effects, manuka honey is known to reduce virulence, motility, and biofilm formation. With this

Evaluating the risks of clinical research: direct comparative analysis.

Science.gov (United States)

Rid, Annette; Abdoler, Emily; Roberson-Nay, Roxann; Pine, Daniel S; Wendler, David

2014-09-01

Many guidelines and regulations allow children and adolescents to be enrolled in research without the prospect of clinical benefit when it poses minimal risk. However, few systematic methods exist to determine when research risks are minimal. This situation has led to significant variation in minimal risk judgments, raising concern that some children are not being adequately protected. To address this concern, we describe a new method for implementing the widely endorsed "risks of daily life" standard for minimal risk. This standard defines research risks as minimal when they do not exceed the risks posed by daily life activities or routine examinations. This study employed a conceptual and normative analysis, and use of an illustrative example. Different risks are composed of the same basic elements: Type, likelihood, and magnitude of harm. Hence, one can compare the risks of research and the risks of daily life by comparing the respective basic elements with each other. We use this insight to develop a systematic method, direct comparative analysis, for implementing the "risks of daily life" standard for minimal risk. The method offers a way of evaluating research procedures that pose the same types of risk as daily life activities, such as the risk of experiencing anxiety, stress, or other psychological harm. We thus illustrate how direct comparative analysis can be applied in practice by using it to evaluate whether the anxiety induced by a respiratory CO2 challenge poses minimal or greater than minimal risks in children and adolescents. Direct comparative analysis is a systematic method for applying the "risks of daily life" standard for minimal risk to research procedures that pose the same types of risk as daily life activities. It thereby offers a method to protect children and adolescents in research, while ensuring that important studies are not blocked because of unwarranted concerns about research risks.

Mechanistic pathways of recognition of a solvent-inaccessible cavity of protein by a ligand

Science.gov (United States)

Mondal, Jagannath; Pandit, Subhendu; Dandekar, Bhupendra; Vallurupalli, Pramodh

One of the puzzling questions in the realm of protein-ligand recognition is how a solvent-inaccessible hydrophobic cavity of a protein gets recognized by a ligand. We address the topic by simulating, for the first time, the complete binding process of benzene from aqueous media to the well-known buried cavity of L99A T4 Lysozyme at an atomistic resolution. Our multiple unbiased microsecond-long trajectories, which were completely blind to the location of target binding site, are able to unequivocally identify the kinetic pathways along which benzene molecule meanders across the solvent and protein and ultimately spontaneously recognizes the deeply buried cavity of L99A T4 Lysozyme at an accurate precision. Our simulation, combined with analysis based on markov state model and free energy calculation, reveals that there are more than one distinct ligand binding pathways. Intriguingly, each of the identified pathways involves the transient opening of a channel of the protein prior to ligand binding. The work will also decipher rich mechanistic details on unbinding kinetics of the ligand as obtained from enhanced sampling techniques.

A comparative study of three different gene expression analysis methods.

Science.gov (United States)

Choe, Jae Young; Han, Hyung Soo; Lee, Seon Duk; Lee, Hanna; Lee, Dong Eun; Ahn, Jae Yun; Ryoo, Hyun Wook; Seo, Kang Suk; Kim, Jong Kun

2017-12-04

TNF-α regulates immune cells and acts as an endogenous pyrogen. Reverse transcription polymerase chain reaction (RT-PCR) is one of the most commonly used methods for gene expression analysis. Among the alternatives to PCR, loop-mediated isothermal amplification (LAMP) shows good potential in terms of specificity and sensitivity. However, few studies have compared RT-PCR and LAMP for human gene expression analysis. Therefore, in the present study, we compared one-step RT-PCR, two-step RT-LAMP and one-step RT-LAMP for human gene expression analysis. We compared three gene expression analysis methods using the human TNF-α gene as a biomarker from peripheral blood cells. Total RNA from the three selected febrile patients were subjected to the three different methods of gene expression analysis. In the comparison of three gene expression analysis methods, the detection limit of both one-step RT-PCR and one-step RT-LAMP were the same, while that of two-step RT-LAMP was inferior. One-step RT-LAMP takes less time, and the experimental result is easy to determine. One-step RT-LAMP is a potentially useful and complementary tool that is fast and reasonably sensitive. In addition, one-step RT-LAMP could be useful in environments lacking specialized equipment or expertise.

Problems in mechanistic theoretical models for cell transformation by ionizing radiation

International Nuclear Information System (INIS)

Chatterjee, Aloke; Holley, W.R.

1992-01-01

A mechanistic model based on yields of double strand breaks has been developed to determine the dose response curves for cell transformation frequencies. At its present stage the model is applicable to immortal cell lines and to various qualities (X-rays, Neon and Iron) of ionizing radiation. Presently, we have considered four types of processes which can lead to activation phenomena: (i) point mutation events on a regulatory segment of selected oncogenes, (ii) inactivation of suppressor genes, through point mutation, (iii) deletion of a suppressor gene by a single track, and (iv) deletion of a suppressor gene by two tracks. (author)

Bluetooth security attacks comparative analysis, attacks, and countermeasures

CERN Document Server

Haataja, Keijo; Pasanen, Sanna; Toivanen, Pekka

2013-01-01

This overview of Bluetooth security examines network vulnerabilities and offers a comparative analysis of recent security attacks. It also examines related countermeasures and proposes a novel attack that works against all existing Bluetooth versions.

Comparative analysis of the mitochondrial genomes in gastropods

International Nuclear Information System (INIS)

Arquez, Moises; Uribe, Juan Esteban; Castro, Lyda Raquel

2012-01-01

In this work we presented a comparative analysis of the mitochondrial genomes in gastropods. Nucleotide and amino acids composition was calculated and a comparative visual analysis of the start and termination codons was performed. The organization of the genome was compared calculating the number of intergenic sequences, the location of the genes and the number of reorganized genes (breakpoints) in comparison with the sequence that is presumed to be ancestral for the group. In order to calculate variations in the rates of molecular evolution within the group, the relative rate test was performed. In spite of the differences in the size of the genomes, the amino acids number is conserved. The nucleotide and amino acid composition is similar between Vetigastropoda, Ceanogastropoda and Neritimorpha in comparison to Heterobranchia and Patellogastropoda. The mitochondrial genomes of the group are very compact with few intergenic sequences, the only exception is the genome of Patellogastropoda with 26,828 bp. Start codons of the Heterobranchia and Patellogastropoda are very variable and there is also an increase in genome rearrangements for these two groups. Generally, the hypothesis of constant rates of molecular evolution between the groups is rejected, except when the genomes of Caenogastropoda and Vetigastropoda are compared.

Comparative analysis of technical efficiencies between compound ...

African Journals Online (AJOL)

This study was designed to compare the level of technical efficiency in the compound and non compound farms in Imo state. A multi-stage random sampling technique was used to select 120 food crop farmers from two out of the three agricultural zones in Imo state. Using the Chow (1960) analysis of covariance technique ...

Productivity of "collisions generate heat" for reconciling an energy model with mechanistic reasoning: A case study

Science.gov (United States)

Scherr, Rachel E.; Robertson, Amy D.

2015-06-01

We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a byproduct of individual particle collisions, which is represented in science education research literature as an obstacle to learning. We demonstrate that in this instructional context, the idea that individual particle collisions generate thermal energy is not an obstacle to learning, but instead is productive: it initiates intellectual progress. Specifically, this idea initiates the reconciliation of the teachers' energy model with mechanistic reasoning about adiabatic compression, and leads to a canonically correct model of the transformation of kinetic energy into thermal energy. We claim that the idea's productivity is influenced by features of our particular instructional context, including the instructional goals of the course, the culture of collaborative sense making, and the use of certain representations of energy.

Mechanistic studies of copper(I)-catalyzed 1,3-halogen migration.

Science.gov (United States)

Van Hoveln, Ryan; Hudson, Brandi M; Wedler, Henry B; Bates, Desiree M; Le Gros, Gabriel; Tantillo, Dean J; Schomaker, Jennifer M

2015-04-29

An ongoing challenge in modern catalysis is to identify and understand new modes of reactivity promoted by earth-abundant and inexpensive first-row transition metals. Herein, we report a mechanistic study of an unusual copper(I)-catalyzed 1,3-migration of 2-bromostyrenes that reincorporates the bromine activating group into the final product with concomitant borylation of the aryl halide bond. A combination of experimental and computational studies indicated this reaction does not involve any oxidation state changes at copper; rather, migration occurs through a series of formal sigmatropic shifts. Insight provided from these studies will be used to expand the utility of aryl copper species in synthesis and develop new ligands for enantioselective copper-catalyzed halogenation.

"Gum bug, leave my heart alone!"--epidemiologic and mechanistic evidence linking periodontal infections and atherosclerosis.

Science.gov (United States)

Kebschull, M; Demmer, R T; Papapanou, P N

2010-09-01

Evidence from epidemiologic studies suggests that periodontal infections are independently associated with subclinical and clinical atherosclerotic vascular disease. Although the strength of the reported associations is modest, the consistency of the data across diverse populations and a variety of exposure and outcome variables suggests that the findings are not spurious or attributable only to the effects of confounders. Analysis of limited data from interventional studies suggests that periodontal treatment generally results in favorable effects on subclinical markers of atherosclerosis, although such analysis also indicates considerable heterogeneity in responses. Experimental mechanistic in vitro and in vivo studies have established the plausibility of a link between periodontal infections and atherogenesis, and have identified biological pathways by which these effects may be mediated. However, the utilized models are mostly mono-infections of host cells by a limited number of 'model' periodontal pathogens, and therefore may not adequately portray human periodontitis as a polymicrobial, biofilm-mediated disease. Future research must identify in vivo pathways in humans that may (i) lead to periodontitis-induced atherogenesis, or (ii) result in treatment-induced reduction of atherosclerosis risk. Data from these studies will be essential for determining whether periodontal interventions have a role in the primary or secondary prevention of atherosclerosis.

Comparative Analysis on Chemical Composition of Bentonite Clays ...

African Journals Online (AJOL)

2017-09-12

Sep 12, 2017 ... Comparative Analysis on Chemical Composition of Bentonite Clays. Obtained from Ashaka and ... versatile material for geotechnical engineering and as well as their demand for ..... A PhD thesis submitted to the Chemical ...

Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design.

Science.gov (United States)

Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M

2016-05-05

Molecular imaging agent design involves simultaneously optimizing multiple probe properties. While several desired characteristics are straightforward, including high affinity and low non-specific background signal, in practice there are quantitative trade-offs between these properties. These include plasma clearance, where fast clearance lowers background signal but can reduce target uptake, and binding, where high affinity compounds sometimes suffer from lower stability or increased non-specific interactions. Further complicating probe development, many of the optimal parameters vary depending on both target tissue and imaging agent properties, making empirical approaches or previous experience difficult to translate. Here, we focus on low molecular weight compounds targeting extracellular receptors, which have some of the highest contrast values for imaging agents. We use a mechanistic approach to provide a quantitative framework for weighing trade-offs between molecules. Our results show that specific target uptake is well-described by quantitative simulations for a variety of targeting agents, whereas non-specific background signal is more difficult to predict. Two in vitro experimental methods for estimating background signal in vivo are compared - non-specific cellular uptake and plasma protein binding. Together, these data provide a quantitative method to guide probe design and focus animal work for more cost-effective and time-efficient development of molecular imaging agents.

Protective Effects of Dihydromyricetin against •OH-Induced Mesenchymal Stem Cells Damage and Mechanistic Chemistry

Directory of Open Access Journals (Sweden)

Xican Li

2016-05-01

Full Text Available As a natural flavonoid in Ampelopsis grossedentata, dihydromyricetin (DHM, 2R,3R-3,5,7,3′,4′,5′-hexahydroxy-2,3-dihydroflavonol was observed to increase the viability of •OH-treated mesenchymal stem cells using a MTT [3-(4,5-dimethylthiazol-2-yl-2,5-diphenyl] assay and flow cytometry analysis. This protective effect indicates DHM may be a beneficial agent for cell transplantation therapy. Mechanistic chemistry studies indicated that compared with myricetin, DHM was less effective at ABTS+• (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid radical scavenging and reducing Cu2+, and had higher •O2− and DPPH• (1,1-diphenyl-2-picrylhydrazyl radical scavenging activities. Additionally, DHM could also chelate Fe2+ to give an absorption maximum at 589 nm. Hence, such protective effect of DHM may arise from its antioxidant activities which are thought to occur via direct radical-scavenging and Fe2+-chelation. Direct radical-scavenging involves an electron transfer (ET pathway. The hydrogenation of the 2,3-double bond is hypothesized to reduce the ET process by blocking the formation of a larger π-π conjugative system. The glycosidation of the 3–OH in myricitrin is assumed to sterically hinder atom transfer in the •O2− and DPPH• radical-scavenging processes. In DHM, the Fe2+-chelating effect can actually be attributed to the 5,3′,4′,5′–OH and 4–C=O groups, and the 3–OH group itself can neither scavenge radicals nor chelate metal.

Structural, mechanistic and functional insight into gliotoxin bis-thiomethylation in Aspergillus fumigatus.

Science.gov (United States)

Dolan, Stephen K; Bock, Tobias; Hering, Vanessa; Owens, Rebecca A; Jones, Gary W; Blankenfeldt, Wulf; Doyle, Sean

2017-02-01

Gliotoxin is an epipolythiodioxopiperazine (ETP) class toxin, contains a disulfide bridge that mediates its toxic effects via redox cycling and is produced by the opportunistic fungal pathogen Aspergillus fumigatus Self-resistance against gliotoxin is effected by the gliotoxin oxidase GliT, and attenuation of gliotoxin biosynthesis is catalysed by gliotoxin S -methyltransferase GtmA. Here we describe the X-ray crystal structures of GtmA-apo (1.66 Å), GtmA complexed to S -adenosylhomocysteine (1.33 Å) and GtmA complexed to S -adenosylmethionine (2.28 Å), providing mechanistic insights into this important biotransformation. We further reveal that simultaneous elimination of the ability of A. fumigatus to dissipate highly reactive dithiol gliotoxin, via deletion of GliT and GtmA, results in the most significant hypersensitivity to exogenous gliotoxin observed to date. Indeed, quantitative proteomic analysis of Δ gliT ::Δ gtmA reveals an uncontrolled over-activation of the gli -cluster upon gliotoxin exposure. The data presented herein reveal, for the first time, the extreme risk associated with intracellular dithiol gliotoxin biosynthesis-in the absence of an efficient dismutation capacity. Significantly, a previously concealed protective role for GtmA and functionality of ETP bis -thiomethylation as an ancestral protection strategy against dithiol compounds is now evident. © 2017 The Authors.

Disruption of steroidogenesis: Cell models for mechanistic investigations and as screening tools.

Science.gov (United States)

Odermatt, Alex; Strajhar, Petra; Engeli, Roger T

2016-04-01

In the modern world, humans are exposed during their whole life to a large number of synthetic chemicals. Some of these chemicals have the potential to disrupt endocrine functions and contribute to the development and/or progression of major diseases. Every year approximately 1000 novel chemicals, used in industrial production, agriculture, consumer products or as pharmaceuticals, are reaching the market, often with limited safety assessment regarding potential endocrine activities. Steroids are essential endocrine hormones, and the importance of the steroidogenesis pathway as a target for endocrine disrupting chemicals (EDCs) has been recognized by leading scientists and authorities. Cell lines have a prominent role in the initial stages of toxicity assessment, i.e. for mechanistic investigations and for the medium to high throughput analysis of chemicals for potential steroidogenesis disrupting activities. Nevertheless, the users have to be aware of the limitations of the existing cell models in order to apply them properly, and there is a great demand for improved cell-based testing systems and protocols. This review intends to provide an overview of the available cell lines for studying effects of chemicals on gonadal and adrenal steroidogenesis, their use and limitations, as well as the need for future improvements of cell-based testing systems and protocols. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rotary ultrasonic machining of CFRP: a mechanistic predictive model for cutting force.

Science.gov (United States)

Cong, W L; Pei, Z J; Sun, X; Zhang, C L

2014-02-01

Cutting force is one of the most important output variables in rotary ultrasonic machining (RUM) of carbon fiber reinforced plastic (CFRP) composites. Many experimental investigations on cutting force in RUM of CFRP have been reported. However, in the literature, there are no cutting force models for RUM of CFRP. This paper develops a mechanistic predictive model for cutting force in RUM of CFRP. The material removal mechanism of CFRP in RUM has been analyzed first. The model is based on the assumption that brittle fracture is the dominant mode of material removal. CFRP micromechanical analysis has been conducted to represent CFRP as an equivalent homogeneous material to obtain the mechanical properties of CFRP from its components. Based on this model, relationships between input variables (including ultrasonic vibration amplitude, tool rotation speed, feedrate, abrasive size, and abrasive concentration) and cutting force can be predicted. The relationships between input variables and important intermediate variables (indentation depth, effective contact time, and maximum impact force of single abrasive grain) have been investigated to explain predicted trends of cutting force. Experiments are conducted to verify the model, and experimental results agree well with predicted trends from this model. Copyright © 2013 Elsevier B.V. All rights reserved.

ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

Science.gov (United States)

Kayala, Matthew A; Baldi, Pierre

2012-10-22

Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

The Constant Comparative Analysis Method Outside of Grounded Theory

Science.gov (United States)

Fram, Sheila M.

2013-01-01

This commentary addresses the gap in the literature regarding discussion of the legitimate use of Constant Comparative Analysis Method (CCA) outside of Grounded Theory. The purpose is to show the strength of using CCA to maintain the emic perspective and how theoretical frameworks can maintain the etic perspective throughout the analysis. My…

A mechanistic model for electricity consumption on dairy farms: Definition, validation, and demonstration

OpenAIRE

Upton, J.R.; Murphy, M.; Shallo, L.; Groot Koerkamp, P.W.G.; Boer, de, I.J.M.

2014-01-01

Our objective was to define and demonstrate a mechanistic model that enables dairy farmers to explore the impact of a technical or managerial innovation on electricity consumption, associated CO2 emissions, and electricity costs. We, therefore, (1) defined a model for electricity consumption on dairy farms (MECD) capable of simulating total electricity consumption along with related CO2 emissions and electricity costs on dairy farms on a monthly basis; (2) validated the MECD using empirical d...

Embryotoxic and pharmacologic potency ranking of six azoles in the rat whole embryo culture by morphological and transcriptomic analysis

International Nuclear Information System (INIS)

Dimopoulou, Myrto; Verhoef, Aart; Pennings, Jeroen L.A.; Ravenzwaay, Bennard van; Rietjens, Ivonne M.C.M.; Piersma, Aldert H.

2017-01-01

Differential gene expression analysis in the rat whole embryo culture (WEC) assay provides mechanistic insight into the embryotoxicity of test compounds. In our study, we hypothesized that comparative analysis of the transcriptomes of rat embryos exposed to six azoles (flusilazole, triadimefon, ketoconazole, miconazole, difenoconazole and prothioconazole) could lead to a better mechanism-based understanding of their embryotoxicity and pharmacological action. For evaluating embryotoxicity, we applied the total morphological scoring system (TMS) in embryos exposed for 48 h. The compounds tested showed embryotoxicity in a dose-response fashion. Functional analysis of differential gene expression after 4 h exposure at the ID 10 (effective dose for 10% decreased TMS), revealed the sterol biosynthesis pathway and embryonic development genes, dominated by genes in the retinoic acid (RA) pathway, albeit in a differential way. Flusilazole, ketoconazole and triadimefon were the most potent compounds affecting the RA pathway, while in terms of regulation of sterol function, difenoconazole and ketoconazole showed the most pronounced effects. Dose-dependent analysis of the effects of flusilazole revealed that the RA pathway related genes were already differentially expressed at low dose levels while the sterol pathway showed strong regulation at higher embryotoxic doses, suggesting that this pathway is less predictive for the observed embryotoxicity. A similar analysis at the 24-hour time point indicated an additional time-dependent difference in the aforementioned pathways regulated by flusilazole. In summary, the rat WEC assay in combination with transcriptomics could add a mechanistic insight into the embryotoxic potency ranking and pharmacological mode of action of the tested compounds. - Highlights: • Embryonic exposure to azoles revealed concentration-dependent malformations. • Transcriptomics could enhance the mechanistic knowledge of embryotoxicants. • Retinoic

Embryotoxic and pharmacologic potency ranking of six azoles in the rat whole embryo culture by morphological and transcriptomic analysis

Energy Technology Data Exchange (ETDEWEB)

Dimopoulou, Myrto, E-mail: myrto.dimopoulou@wur.nl [Division of Toxicology, Wageningen University (Netherlands); National Institute of Public Health and the Environment (RIVM), Bilthoven (Netherlands); Verhoef, Aart; Pennings, Jeroen L.A. [National Institute of Public Health and the Environment (RIVM), Bilthoven (Netherlands); Ravenzwaay, Bennard van [Division of Toxicology, Wageningen University (Netherlands); BASF SE, Experimental Toxicology and Ecology, Ludwigshafen (Germany); Rietjens, Ivonne M.C.M. [Division of Toxicology, Wageningen University (Netherlands); Piersma, Aldert H. [National Institute of Public Health and the Environment (RIVM), Bilthoven (Netherlands); Institute for Risk Assessment Sciences, Utrecht University, Utrecht (Netherlands)

2017-05-01

Differential gene expression analysis in the rat whole embryo culture (WEC) assay provides mechanistic insight into the embryotoxicity of test compounds. In our study, we hypothesized that comparative analysis of the transcriptomes of rat embryos exposed to six azoles (flusilazole, triadimefon, ketoconazole, miconazole, difenoconazole and prothioconazole) could lead to a better mechanism-based understanding of their embryotoxicity and pharmacological action. For evaluating embryotoxicity, we applied the total morphological scoring system (TMS) in embryos exposed for 48 h. The compounds tested showed embryotoxicity in a dose-response fashion. Functional analysis of differential gene expression after 4 h exposure at the ID{sub 10} (effective dose for 10% decreased TMS), revealed the sterol biosynthesis pathway and embryonic development genes, dominated by genes in the retinoic acid (RA) pathway, albeit in a differential way. Flusilazole, ketoconazole and triadimefon were the most potent compounds affecting the RA pathway, while in terms of regulation of sterol function, difenoconazole and ketoconazole showed the most pronounced effects. Dose-dependent analysis of the effects of flusilazole revealed that the RA pathway related genes were already differentially expressed at low dose levels while the sterol pathway showed strong regulation at higher embryotoxic doses, suggesting that this pathway is less predictive for the observed embryotoxicity. A similar analysis at the 24-hour time point indicated an additional time-dependent difference in the aforementioned pathways regulated by flusilazole. In summary, the rat WEC assay in combination with transcriptomics could add a mechanistic insight into the embryotoxic potency ranking and pharmacological mode of action of the tested compounds. - Highlights: • Embryonic exposure to azoles revealed concentration-dependent malformations. • Transcriptomics could enhance the mechanistic knowledge of embryotoxicants. �

Comparative analysis of direct and indirect property investment ...

African Journals Online (AJOL)

Comparative analysis of direct and indirect property investment returns in Abuja. ... in property shares is more risky than commercial property due to the risk ... of the stock market, it was discovered that there is a strong positive relationship ...

Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications

Directory of Open Access Journals (Sweden)

Broglie Karen E

2008-09-01

Full Text Available Abstract Background Starch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done. Results The wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations. Conclusion Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs, it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each

Mechanistic model to predict colostrum intake based on deuterium oxide dilution technique data and impact of gestation and prefarrowing diets on piglet intake and sow yield of colostrum

DEFF Research Database (Denmark)

Theil, Peter Kappel; Flummer, Christine; Hurley, W L

2014-01-01

The aims of the present study were to quantify colostrum intake (CI) of piglets using the D2O dilution technique, to develop a mechanistic model to predict CI, to compare these data with CI predicted by a previous empirical predictive model developed for bottle-fed piglets, and to study how...... composition of diets fed to gestating sows affected piglet CI, sow colostrum yield (CY), and colostrum composition. In total, 240 piglets from 40 litters were enriched with D2O. The CI measured by D2O from birth until 24 h after the birth of first-born piglet was on average 443 g (SD 151). Based on measured...... CI, a mechanistic model to predict CI was developed using piglet characteristics (24-h weight gain [WG; g], BW at birth [BWB; kg], and duration of CI [D; min]: CI, g = –106 + 2.26 WG + 200 BWB + 0.111 D – 1,414 WG/D + 0.0182 WG/BWB (R2 = 0.944). This model was used to predict the CI for all colostrum...

Development of a mechanistic model for release of radionuclides from spent fuel in brines: Salt Repository Project

International Nuclear Information System (INIS)

Reimus, P.W.; Windisch, C.F.

1988-03-01

At present there are no comprehensive mechanistic models describing the release of radionuclides from spent fuel in brine environments. This report provides a comprehensive review of the various factors that can affect radionuclide release from spent fuel, suggests a modeling approach, and discusses proposed experiments for obtaining a better mechanistic understanding of the radionuclide release processes. Factors affecting radionuclide release include the amount, location, and disposition of radionuclides in the fuel and environmental factors such as redox potential, pH, the presence of complexing anions, temperature, and radiolysis. It is concluded that a model describing the release of radionuclides from spent fuel should contain separate terms for release from the gap, grain boundaries, and grains of the fuel. Possible functional forms for these terms are discussed in the report. Experiments for assessing their validity and obtaining key model parameters are proposed. 71 refs., 4 figs., 6 tabs

Productivity of "Collisions Generate Heat" for Reconciling an Energy Model with Mechanistic Reasoning: A Case Study

Science.gov (United States)

Scherr, Rachel E.; Robertson, Amy D.

2015-01-01

We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a…

Synthetic and mechanistic aspects of titanium-mediated carbonyl olefinations

Energy Technology Data Exchange (ETDEWEB)

Petasis, N.A.; Staszewski, J.P.; Hu, Yong-Han; Lu, Shao-Po [Univ. of Southern California, Los Angeles, CA (United States)

1995-12-31

A new method for the olefination of carbonyl compounds with dimethyl titanocene, and other related bishydrocarbyl titanocene derivatives has been recently developed in the author`s laboratories. This process is experimentally convenient and works with various types of carbonyl compounds, including aldehydes, ketones, esters, lactones, carbonates, anhydrides, amides, imides, lactams, thioesters, selenoesters, and acylsilanes. More recent studies have focused on the scope and utility of this reaction, including mechanistic studies and synthetic applications. In addition to varying the reaction conditions, the authors have examined several mixed titanocene derivatives and have found ways for carrying out this type of olefination at room temperature, such as the use of tris(trimethylsilyl) titanacyclobutene. The authors have also employed this reaction in the modification of carbohydrates and cyclobutenediones. This olefination was also followed-up with subsequent transformations to produce carbocycles and heterocycles, including tetrahydrofurans and tetrahydropyrans.

Religious Education in Russia: A Comparative and Critical Analysis

Science.gov (United States)

Blinkova, Alexandra; Vermeer, Paul

2018-01-01

RE in Russia has been recently introduced as a compulsory regular school subject during the last year of elementary school. The present study offers a critical analysis of the current practice of Russian RE by comparing it with RE in Sweden, Denmark and Britain. This analysis shows that Russian RE is ambivalent. Although it is based on a…

Greenfields and acquisitions: a comparative analysis

Directory of Open Access Journals (Sweden)

Nicolae MARINESCU

2016-07-01

Full Text Available This paper compares greenfields and acquisitions as foreign direct investment (FDI alternatives used by transnational corporations (TNCs. First, the determinants leading to the choice of companies between the two modes of entry into a foreign market are laid out. Then, specific features of each alternative are highlighted, by contrasting the advantages and disadvantages of both types of FDI. Based on this analysis, some conclusions are drawn in the end concerning the most important factors that influence the decision of a company whether to choose a greenfield investment or an acquisition.

A nested mechanistic sub-study into the effect of tranexamic acid versus placebo on intracranial haemorrhage and cerebral ischaemia in isolated traumatic brain injury: study protocol for a randomised controlled trial (CRASH-3 Trial Intracranial Bleeding Mechanistic Sub-Study [CRASH-3 IBMS]).

Science.gov (United States)

Mahmood, Abda; Roberts, Ian; Shakur, Haleema

2017-07-17

Tranexamic acid prevents blood clots from breaking down and reduces bleeding. However, it is uncertain whether tranexamic acid is effective in traumatic brain injury. The CRASH-3 trial is a randomised controlled trial that will examine the effect of tranexamic acid (versus placebo) on death and disability in 13,000 patients with traumatic brain injury. The CRASH-3 trial hypothesizes that tranexamic acid will reduce intracranial haemorrhage, which will reduce the risk of death. Although it is possible that tranexamic acid will reduce intracranial bleeding, there is also a potential for harm. In particular, tranexamic acid may increase the risk of cerebral thrombosis and ischaemia. The protocol detailed here is for a mechanistic sub-study nested within the CRASH-3 trial. This mechanistic sub-study aims to examine the effect of tranexamic acid (versus placebo) on intracranial bleeding and cerebral ischaemia. The CRASH-3 Intracranial Bleeding Mechanistic Sub-Study (CRASH-3 IBMS) is nested within a prospective, double-blind, multi-centre, parallel-arm randomised trial called the CRASH-3 trial. The CRASH-3 IBMS will be conducted in a cohort of approximately 1000 isolated traumatic brain injury patients enrolled in the CRASH-3 trial. In the CRASH-3 IBMS, brain scans acquired before and after randomisation are examined, using validated methods, for evidence of intracranial bleeding and cerebral ischaemia. The primary outcome is the total volume of intracranial bleeding measured on computed tomography after randomisation, adjusting for baseline bleeding volume. Secondary outcomes include progression of intracranial haemorrhage (from pre- to post-randomisation scans), new intracranial haemorrhage (seen on post- but not pre-randomisation scans), intracranial haemorrhage following neurosurgery, and new focal ischaemic lesions (seen on post-but not pre-randomisation scans). A linear regression model will examine whether receipt of the trial treatment can predict haemorrhage

MECHANISTIC STUDY OF COLCHICINE’s ELECTROCHEMICAL OXIDATION

International Nuclear Information System (INIS)

Bodoki, Ede; Chira, Ruxandra; Zaharia, Valentin; Săndulescu, Robert

2015-01-01

Colchicine, as one of the most ancient drugs of human kind, is still in the focal point of the current research due to its multimodal mechanism of action. The elucidation of colchicine’s still unknown redox properties may play an important role in deciphering its beneficial and harmful implications over the human body. Therefore, a systematic mechanistic study of colchicine’s oxidation has been undertaken by electrochemistry coupled to mass spectrometry using two different types of electrolytic cells, in order to clarify the existing inconsistencies with respect to this topic. At around 1 V vs. Pd/H 2 , initiated by a one-electron transfer, the oxidation of colchicine sets off leading to a cation radical, whose further oxidation may evolve on several different pathways. The main product of the anodic electrochemical reaction, regardless of the carrier solution’s pH is represented by a 7-hydroxy derivative of colchicine. At more anodic potentials (above 1.4 V vs. Pd/H 2 ) compounds arising from epoxidation and/or multiple hydroxylation occur. No di- or tridemethylated quinone structures, as previously suggested in the literature for the electrolytic oxidation of colchicine, has been detected in the mass spectra.

Mechanistic Studies on the Copper-Catalyzed N-Arylation of Amides

Science.gov (United States)

Strieter, Eric R.; Bhayana, Brijesh; Buchwald, Stephen L.

2009-01-01

The copper-catalyzed N-arylation of amides, i.e., the Goldberg reaction, is an efficient method for the construction of products relevant to both industry and academic settings. Herein, we present mechanistic details concerning the catalytic and stoichiometric N-arylation of amides. In the context of the catalytic reaction, our findings reveal the importance of chelating diamine ligands in controlling the concentration of the active catalytic species. The consistency between the catalytic and stoichiometric results suggest that the activation of aryl halides occurs through a 1,2-diamine-ligated copper(I) amidate complex. Kinetic studies on the stoichiometric N-arylation of aryl iodides using 1,2-diamine ligated Cu(I) amidates also provide insights into the mechanism of aryl halide activation. PMID:19072233

DFT Mechanistic Study of the Selective Terminal C-H Activation of n-Pentane with a Tungsten Allyl Nitrosyl Complex

KAUST Repository

Lee, Richmond

2017-01-17

Mechanistic insights into the selective C-H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using Bader’s atom in molecules (AIM) analysis on the elementary steps of the hydrogen transfer process, TS1 and TS2, it was observed that the calculated H-transfer models were closely similar to Hall’s metal-assisted σ-bond metathesis through bond critical point (BCP) comparisons. One distinguishable feature was the fact that the formal oxidation state of the W changed in the concerted H-transfer process. To better differentiate, we term these processes as ‘Formal Reductive Hydrogen Transfer’ (FRHT) for TS1 and ‘Formal Oxidative Hydrogen Transfer’ (FOHT) for TS2.

DFT Mechanistic Study of the Selective Terminal C-H Activation of n-Pentane with a Tungsten Allyl Nitrosyl Complex

KAUST Repository

Lee, Richmond; Tan, Davin; Liu, Chaoli; Li, Huaifeng; Guo, Hao; Shyue, Jing-Jong; Huang, Kuo-Wei

2017-01-01

Mechanistic insights into the selective C-H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using Bader’s atom in molecules (AIM) analysis on the elementary steps of the hydrogen transfer process, TS1 and TS2, it was observed that the calculated H-transfer models were closely similar to Hall’s metal-assisted σ-bond metathesis through bond critical point (BCP) comparisons. One distinguishable feature was the fact that the formal oxidation state of the W changed in the concerted H-transfer process. To better differentiate, we term these processes as ‘Formal Reductive Hydrogen Transfer’ (FRHT) for TS1 and ‘Formal Oxidative Hydrogen Transfer’ (FOHT) for TS2.

Mechanistic kinetic modeling generates system-independent P-glycoprotein mediated transport elementary rate constants for inhibition and, in combination with 3D SIM microscopy, elucidates the importance of microvilli morphology on P-glycoprotein mediated efflux activity.

Science.gov (United States)

Ellens, Harma; Meng, Zhou; Le Marchand, Sylvain J; Bentz, Joe

2018-06-01

In vitro transporter kinetics are typically analyzed by steady-state Michaelis-Menten approximations. However, no clear evidence exists that these approximations, applied to multiple transporters in biological membranes, yield system-independent mechanistic parameters needed for reliable in vivo hypothesis generation and testing. Areas covered: The classical mass action model has been developed for P-glycoprotein (P-gp) mediated transport across confluent polarized cell monolayers. Numerical integration of the mass action equations for transport using a stable global optimization program yields fitted elementary rate constants that are system-independent. The efflux active P-gp was defined by the rate at which P-gp delivers drugs to the apical chamber, since as much as 90% of drugs effluxed by P-gp partition back into nearby microvilli prior to reaching the apical chamber. The efflux active P-gp concentration was 10-fold smaller than the total expressed P-gp for Caco-2 cells, due to their microvilli membrane morphology. The mechanistic insights from this analysis are readily extrapolated to P-gp mediated transport in vivo. Expert opinion: In vitro system-independent elementary rate constants for transporters are essential for the generation and validation of robust mechanistic PBPK models. Our modeling approach and programs have broad application potential. They can be used for any drug transporter with minor adaptations.

Kinetics and Mechanistic Chemistry of Oxidation of Butacaine Sulfate by Chloramine-B in Acid Medium

International Nuclear Information System (INIS)

Shubha, Jayachamarajapura Pranesh; Kotabagi, Vinutha; Puttaswamy

2012-01-01

Butacaine sulfate is an ester of p-aminobenzoic acid which has been widely used as a local anaesthetic and it is a long standing agent particularly for spinal anaesthesia. For this reason, a kinetic study of oxidation of butacaine sulfate by sodium N-chlorobenzenesulfonamide (chloramine-B or CAB) has been carried out in HClO 4 medium at 303 K in order to explore this redox system mechanistic chemistry. The rate shows a first-order dependence on both [CAB] o , and [substrate] o , and a fractional-order dependence on acid concentration. Decrease of dielectric constant of the medium, by adding methanol, increases the rate of the reaction. Variation of ionic strength and addition of benzenesulfonamide or NaCl have no significant effect on the rate. The reaction was studied at different temperatures and the activation parameters have been evaluated. The stoichiometry of the reaction has been found to be 1:2 and the oxidation products have been identified by spectral analysis. The observed results have been explained by plausible mechanism and the related rate law has been deduced

COGNAT: a web server for comparative analysis of genomic neighborhoods.

Science.gov (United States)

Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

2017-11-22

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

Mechanistic, Mutational, and Structural Evaluation of a Taxus Phenylalanine Aminomutase

Energy Technology Data Exchange (ETDEWEB)

Feng, Lei; Wanninayake, Udayanga; Strom, Susan; Geiger, James; Walker, Kevin D. (MSU)

2014-10-02

The structure of a phenylalanine aminomutase (TcPAM) from Taxus canadensis has been determined at 2.4 {angstrom} resolution. The active site of the TcPAM contains the signature 4-methylidene-1H-imidazol-5(4H)-one prosthesis, observed in all catalysts of the class I lyase-like family. This catalyst isomerizes (S)-{alpha}-phenylalanine to the (R)-{beta}-isomer by exchange of the NH{sub 2}/H pair. The stereochemistry of the TcPAM reaction product is opposite of the (S)-{beta}-tyrosine made by the mechanistically related tyrosine aminomutase (SgTAM) from Streptomyces globisporus. Since TcPAM and SgTAM share similar tertiary- and quaternary-structures and have several highly conserved aliphatic residues positioned analogously in their active sites for substrate recognition, the divergent product stereochemistries of these catalysts likely cannot be explained by differences in active site architecture. The active site of the TcPAM structure also is in complex with (E)-cinnamate; the latter functions as both a substrate and an intermediate. To account for the distinct (3R)-{beta}-amino acid stereochemistry catalyzed by TcPAM, the cinnamate skeleton must rotate the C{sub 1}-C{sub {alpha}} and C{sub ipso}-C{sub {beta}} bonds 180{sup o} in the active site prior to exchange and rebinding of the NH{sub 2}/H pair to the cinnamate, an event that is not required for the corresponding acrylate intermediate in the SgTAM reaction. Moreover, the aromatic ring of the intermediate makes only one direct hydrophobic interaction with Leu-104. A L104A mutant of TcPAM demonstrated an 1.5-fold increase in k{sub cat} and a decrease in K{sub M} values for sterically demanding 3'-methyl-{alpha}-phenylalanine and styryl-{alpha}-alanine substrates, compared to the kinetic parameters for TcPAM. These parameters did not change significantly for the mutant with 4'-methyl-{alpha}-phenylalanine compared to those for TcPAM.

This Mechanistic Step Is ''Productive'': Organic Chemistry Students' Backward-Oriented Reasoning

Science.gov (United States)

Caspari, I.; Weinrich, M. L.; Sevian, H.; Graulich, N.

2018-01-01

If an organic chemistry student explains that she represents a mechanistic step because ''it's a productive part of the mechanism,'' what meaning could the professor teaching the class attribute to this statement, what is actually communicated, and what does it mean for the student? The professor might think that the explanation is based on…

Fetal programming of CVD and renal disease: animal models and mechanistic considerations.

Science.gov (United States)

Langley-Evans, Simon C

2013-08-01

The developmental origins of health and disease hypothesis postulates that exposure to a less than optimal maternal environment during fetal development programmes physiological function, and determines risk of disease in adult life. Much evidence of such programming comes from retrospective epidemiological cohorts, which demonstrate associations between birth anthropometry and non-communicable diseases of adulthood. The assertion that variation in maternal nutrition drives these associations is supported by studies using animal models, which demonstrate that maternal under- or over-nutrition during pregnancy can programme offspring development. Typically, the offspring of animals that are undernourished in pregnancy exhibit a relatively narrow range of physiological phenotypes that includes higher blood pressure, glucose intolerance, renal insufficiency and increased adiposity. The observation that common phenotypes arise from very diverse maternal nutritional insults has led to the proposal that programming is driven by a small number of mechanistic processes. The remodelling of tissues during development as a consequence of maternal nutritional status being signalled by endocrine imbalance or key nutrients limiting processes in the fetus may lead to organs having irreversibly altered structures that may limit their function with ageing. It has been proposed that the maternal diet may impact upon epigenetic marks that determine gene expression in fetal tissues, and this may be an important mechanism connecting maternal nutrient intakes to long-term programming of offspring phenotype. The objective for this review is to provide an overview of the mechanistic basis of fetal programming, demonstrating the critical role of animal models as tools for the investigation of programming phenomena.

Modeling Bird Migration under Climate Change: A Mechanistic Approach

Science.gov (United States)

Smith, James A.

2009-01-01

How will migrating birds respond to changes in the environment under climate change? What are the implications for migratory success under the various accelerated climate change scenarios as forecast by the Intergovernmental Panel on Climate Change? How will reductions or increased variability in the number or quality of wetland stop-over sites affect migratory bird species? The answers to these questions have important ramifications for conservation biology and wildlife management. Here, we describe the use of continental scale simulation modeling to explore how spatio-temporal changes along migratory flyways affect en-route migration success. We use an individually based, biophysical, mechanistic, bird migration model to simulate the movement of shorebirds in North America as a tool to study how such factors as drought and wetland loss may impact migratory success and modify migration patterns. Our model is driven by remote sensing and climate data and incorporates important landscape variables. The energy budget components of the model include resting, foraging, and flight, but presently predation is ignored. Results/Conclusions We illustrate our model by studying the spring migration of sandpipers through the Great Plains to their Arctic breeding grounds. Why many species of shorebirds have shown significant declines remains a puzzle. Shorebirds are sensitive to stop-over quality and spacing because of their need for frequent refueling stops and their opportunistic feeding patterns. We predict bird "hydrographs that is, stop-over frequency with latitude, that are in agreement with the literature. Mean stop-over durations predicted from our model for nominal cases also are consistent with the limited, but available data. For the shorebird species simulated, our model predicts that shorebirds exhibit significant plasticity and are able to shift their migration patterns in response to changing drought conditions. However, the question remains as to whether this

Comparative risk analysis for the Rocky Flats Plant integrated project planning

International Nuclear Information System (INIS)

Jones, M.E.; Shain, D.I.

1994-01-01

The Rocky Flats Plant is developing, with active stakeholder a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Final disposition of the Rocky Flats Plant materials and contaminants requires consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs relative risks to workers and the public, and waste disposition. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risks from postulated options or endstates. These postulated options or endstates can be various remedial alternatives, or future endstate uses of federal agency land. Currently, there does not exist any approved methodology that aggregates various incremental risk estimates. Comparative Risk Analysis has been developed to aggregate various incremental risk estimates to develop a site cumulative risk estimate. This paper discusses development of the Comparative Risk Analysis methodology, stakeholder participation and lessons learned from these challenges

In vitro efficiency and mechanistic role of indocyanine green as photodynamic therapy agent for human melanoma

Energy Technology Data Exchange (ETDEWEB)

Mamoon, A.M.; Miller, L.; Gamal-Eldeen, A. M.; Ruppel, M. E.; Smith, R. J.; Tsang, T.; Miller, L. M.

2009-05-02

Photodynamic therapy (PDT) is a promising treatment for superficial cancer. However, poor therapeutic results have been reported for melanoma, due to the high melanin content. Indocyanine green (ICG) has near infrared absorption (700-800 nm) and melanins do not absorb strongly in this area. This study explores the efficiency of ICG as a PDT agent for human melanoma, and its mechanistic role in the cell death pathway. Human skin melanoma cells (Sk-Mel-28) were incubated with ICG and exposed to a low power Ti:Sapphire laser. Synchrotron-assisted Fourier transform infrared microspectroscopy and hierarchical cluster analysis were used to assess the cell damage and changes in lipid, protein, and nucleic acids. The cell death pathway was determined by analysis of cell viability and apoptosis and necrosis markers. In the cell death pathway, {sup 1}O{sub 2} generation evoked rapid multiple consequences that trigger apoptosis after laser exposure for only 15min including the release of cytochrome c, the activation of total caspases, caspase-3, and caspase-9, the inhibition of NF-{Kappa}B P65, and the enhancement of DNA fragmentation, and histone acetylation. ICG/PDT can efficiently and rapidly induce apoptosis in human melanoma cells and it can be considered as a new therapeutic approach for topical treatment of melanoma.

A Comparative Analysis of Motivations for Occupational Choice or ...

African Journals Online (AJOL)

A Comparative Analysis of Motivations for Occupational Choice or Preference between ... The results showed that these factors (external influence, extrinsic ... are drawn, and recommendations made for career counselling of students.

Comparative Analysis of Kernel Methods for Statistical Shape Learning

National Research Council Canada - National Science Library

Rathi, Yogesh; Dambreville, Samuel; Tannenbaum, Allen

2006-01-01

.... In this work, we perform a comparative analysis of shape learning techniques such as linear PCA, kernel PCA, locally linear embedding and propose a new method, kernelized locally linear embedding...

Collection and analysis of existing data for waste tank mechanistic analysis

Energy Technology Data Exchange (ETDEWEB)

Allemann, R.T.; Antoniak, Z.I.; Friley, J.R.; Haines, C.E.; Liljegren, L.M.; Somasundaram, S.

1991-12-01

Pacific Northwest Laboratory (PNL) is conducting this study for Westinghouse Hanford Company (Westinghouse Hanford), a contractor for the US Department of Energy (DOE). The purpose of the work is to study possible mechanisms and fluid dynamics contributing to the periodic release of gases from the double-shell waste storage tanks at the Hanford Site in Richland, Washington. The waste inside the tank is generating and periodically releasing potentially flammable gases into the tank's vent system according to observations. Questions scientists are trying to answer are: (1) How are these gases generated (2) How did these gases become trapped (3) What causes the periodic gas releases (4) And, what is the mechanism of the gas releases To develop a safe mitigation strategy, possible physical mechanisms for the periodic release of flammable gases need to be understood. During initial work, PNL has obtained, correlated, analyzed, and compared data with expected physical properties, defined mechanisms; and prepared initial models of gas formation and retention. This is the second interim report summarizing the status of the work done to data.

Comparative floorplan-analysis as a means to develop design guidelines

NARCIS (Netherlands)

Van Hoogdalem, H.; van der Voordt, D.J.M.; van Wegen, H.B.R.

1985-01-01

This study explores the usefulness of comparative floorplan-analysis for the development of spatio-organizational concepts in architectural design processes. Each floorplan can be considered as a reflection of the goals and activities of the users as interpreted by the architect. By comparing a wide

Comparative study of standard space and real space analysis of quantitative MR brain data.

Science.gov (United States)

Aribisala, Benjamin S; He, Jiabao; Blamire, Andrew M

2011-06-01

To compare the robustness of region of interest (ROI) analysis of magnetic resonance imaging (MRI) brain data in real space with analysis in standard space and to test the hypothesis that standard space image analysis introduces more partial volume effect errors compared to analysis of the same dataset in real space. Twenty healthy adults with no history or evidence of neurological diseases were recruited; high-resolution T(1)-weighted, quantitative T(1), and B(0) field-map measurements were collected. Algorithms were implemented to perform analysis in real and standard space and used to apply a simple standard ROI template to quantitative T(1) datasets. Regional relaxation values and histograms for both gray and white matter tissues classes were then extracted and compared. Regional mean T(1) values for both gray and white matter were significantly lower using real space compared to standard space analysis. Additionally, regional T(1) histograms were more compact in real space, with smaller right-sided tails indicating lower partial volume errors compared to standard space analysis. Standard space analysis of quantitative MRI brain data introduces more partial volume effect errors biasing the analysis of quantitative data compared to analysis of the same dataset in real space. Copyright © 2011 Wiley-Liss, Inc.

Simulating soil C stability with mechanistic systems models: a multisite comparison of measured fractions and modelled pools

Science.gov (United States)

Robertson, Andy; Schipanski, Meagan; Sherrod, Lucretia; Ma, Liwang; Ahuja, Lajpat; McNamara, Niall; Smith, Pete; Davies, Christian

2016-04-01

Agriculture, covering more than 30% of global land area, has an exciting opportunity to help combat climate change by effectively managing its soil to promote increased C sequestration. Further, newly sequestered soil carbon (C) through agriculture needs to be stored in more stable forms in order to have a lasting impact on reducing atmospheric CO2 concentrations. While land uses in different climates and soils require different management strategies, the fundamental mechanisms that regulate C sequestration and stabilisation remain the same. These mechanisms are used by a number of different systems models to simulate C dynamics, and thus assess the impacts of change in management or climate. To evaluate the accuracy of these model simulations, our research uses a multidirectional approach to compare C stocks of physicochemical soil fractions collected at two long-term agricultural sites. Carbon stocks for a number of soil fractions were measured at two sites (Lincoln, UK; Colorado, USA) over 8 and 12 years, respectively. Both sites represent managed agricultural land but have notably different climates and levels of disturbance. The measured soil fractions act as proxies for varying degrees of stability, with C contained within these fractions relatable to the C simulated within the soil pools of mechanistic systems models1. Using stable isotope techniques at the UK site, specific turnover times of C within the different fractions were determined and compared with those simulated in the pools of 3 different models of varying complexity (RothC, DayCent and RZWQM2). Further, C dynamics and N-mineralisation rates of the measured fractions at the US site were assessed and compared to results of the same three models. The UK site saw a significant increase in C stocks within the most stable fractions, with topsoil (0-30cm) sequestration rates of just over 0.3 tC ha-1 yr-1 after only 8 years. Further, the sum of all fractions reported C sequestration rates of nearly 1

Mechanistic understanding of monosaccharide-air flow battery electrochemistry

Science.gov (United States)

Scott, Daniel M.; Tsang, Tsz Ho; Chetty, Leticia; Aloi, Sekotilani; Liaw, Bor Yann

Recently, an inexpensive monosaccharide-air flow battery configuration has been demonstrated to utilize a strong base and a mediator redox dye to harness electrical power from the partial oxidation of glucose. Here the mechanistic understanding of glucose oxidation in this unique glucose-air power source is further explored by acid-base titration experiments, 13C NMR, and comparison of results from chemically different redox mediators (indigo carmine vs. methyl viologen) and sugars (fructose vs. glucose) via studies using electrochemical techniques. Titration results indicate that gluconic acid is the main product of the cell reaction, as supported by evidence in the 13C NMR spectra. Using indigo carmine as the mediator dye and fructose as the energy source, an abiotic cell configuration generates a power density of 1.66 mW cm -2, which is greater than that produced from glucose under similar conditions (ca. 1.28 mW cm -2). A faster transition from fructose into the ene-diol intermediate than from glucose likely contributed to this difference in power density.

Flow-mediated dilation: can new approaches provide greater mechanistic insight into vascular dysfunction in preeclampsia and other diseases?

Science.gov (United States)

Weissgerber, Tracey L

2014-11-01

Endothelial dysfunction is a key feature of preeclampsia and may contribute to increased cardiovascular disease risk years after pregnancy. Flow-mediated dilation (FMD) is a non-invasive endothelial function test that predicts cardiovascular event risk. New protocols allow researchers to measure three components of the FMD response: FMD, low flow-mediated constriction, and shear stimulus. This review encourages researchers to think beyond "low FMD" by examining how these three components may provide additional insights into the mechanisms and location of vascular dysfunction. The review then examines what FMD studies reveal about vascular dysfunction in preeclampsia while highlighting opportunities to gain greater mechanistic insight from new protocols. Studies using traditional protocols show that FMD is low in mid-pregnancy prior to preeclampsia, at diagnosis, and for 3 years post-partum. However, FMD returns to normal by 10 years post-partum. Studies using new protocols are needed to gain more mechanistic insight.

A Comparative Analysis of Fuzzy Inference Engines in Context of ...

African Journals Online (AJOL)

Fuzzy inference engine has found successful applications in a wide variety of fields, such as automatic control, data classification, decision analysis, expert engines, time series prediction, robotics, pattern recognition, etc. This paper presents a comparative analysis of three fuzzy inference engines, max-product, max-min ...

Mechanistic failure mode investigation and resolution of parvovirus retentive filters.

Science.gov (United States)

LaCasse, Daniel; Lute, Scott; Fiadeiro, Marcus; Basha, Jonida; Stork, Matthew; Brorson, Kurt; Godavarti, Ranga; Gallo, Chris

2016-07-08

Virus retentive filters are a key product safety measure for biopharmaceuticals. A simplistic perception is that they function solely based on a size-based particle removal mechanism of mechanical sieving and retention of particles based on their hydrodynamic size. Recent observations have revealed a more nuanced picture, indicating that changes in viral particle retention can result from process pressure and/or flow interruptions. In this study, a mechanistic investigation was performed to help identify a potential mechanism leading to the reported reduced particle retention in small virus filters. Permeate flow rate or permeate driving force were varied and analyzed for their impact on particle retention in three commercially available small virus retentive filters. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:959-970, 2016. © 2016 American Institute of Chemical Engineers.

A mechanistic model for long-term nuclear waste glass dissolution integrating chemical affinity and interfacial diffusion barrier

Energy Technology Data Exchange (ETDEWEB)

Ma, Teqi [Northwest Institute of Nuclear Technology, No.28 Pingyu Road, Baqiao District, Xi' an,Shaanxi, 710024 (China); Mechanics and Physics of Solids Research Group, Modelling and Simulation Centre, The University of Manchester, Oxford Road, Manchester, M13 9PL (United Kingdom); Jivkov, Andrey P., E-mail: andrey.jivkov@manchester.ac.uk [Mechanics and Physics of Solids Research Group, Modelling and Simulation Centre, The University of Manchester, Oxford Road, Manchester, M13 9PL (United Kingdom); Li, Weiping; Liang, Wei; Wang, Yu; Xu, Hui [Northwest Institute of Nuclear Technology, No.28 Pingyu Road, Baqiao District, Xi' an,Shaanxi, 710024 (China); Han, Xiaoyuan, E-mail: xyhan_nint@sina.cn [Northwest Institute of Nuclear Technology, No.28 Pingyu Road, Baqiao District, Xi' an,Shaanxi, 710024 (China)

2017-04-01

Understanding the alteration of nuclear waste glass in geological repository conditions is critical element of the analysis of repository retention function. Experimental observations of glass alterations provide a general agreement on the following regimes: inter-diffusion, hydrolysis process, rate drop, residual rate and, under very particular conditions, resumption of alteration. Of these, the mechanisms controlling the rate drop and the residual rate remain a subject of dispute. This paper offers a critical review of the two most competitive models related to these regimes: affinity–limited dissolution and diffusion barrier. The limitations of these models are highlighted by comparison of their predictions with available experimental evidence. Based on the comprehensive discussion of the existing models, a new mechanistic model is proposed as a combination of the chemical affinity and diffusion barrier concepts. It is demonstrated how the model can explain experimental phenomena and data, for which the existing models are shown to be not fully adequate.

Comparative analysis of wholesale and retail frozen fish marketing ...

African Journals Online (AJOL)

Comparative analysis of wholesale and retail frozen fish marketing in Port Harcourt Metropolis, Rivers State, Nigeria. ... from each market giving 30 retail marketers and 30 wholesale marketers. ... EMAIL FULL TEXT EMAIL FULL TEXT

Comparative analysis of crayfish marketing in selected markets of ...

African Journals Online (AJOL)

Comparative analysis of crayfish marketing in selected markets of Akwa Ibom and Abia States, Nigeria. ... It specifically looked at market integration, costs and return, marketing margin, marketing ... EMAIL FULL TEXT EMAIL FULL TEXT

comparative analysis of some existing kinetic models with proposed

African Journals Online (AJOL)

IGNATIUS NWIDI

two statistical parameters namely; linear regression coefficient of correlation (R2) and ... Keynotes: Heavy metals, Biosorption, Kinetics Models, Comparative analysis, Average Relative Error. 1. ... If the flow rate is low, a simple manual batch.

Crystallographic Analysis and Structural Revision of a ...

African Journals Online (AJOL)

ABSTRACT. Single crystal X-ray analysis of a spiroterpenoid rearrangement product has revealed that its structure is, in fact, isomeric with the structure proposed previously – an observation that has significant mechanistic implications. KEYWORDS. Spiroterpenoid, rearrangement, X-ray crystallography, camphor derivative.

Crystallographic Analysis and Structural Revision of a ...

African Journals Online (AJOL)

Single crystal X-ray analysis of a spiroterpenoid rearrangement product has revealed that its structure is, in fact, isomeric with the structure proposed previously – an observation that has significant mechanistic implications. Keywords: Spiroterpenoid, rearrangement, X-ray crystallography, camphor derivative.

Mechanistic Indicators of Childhood Asthma (MICA): piloting ...

Science.gov (United States)

Background: Modem methods in molecular biology and advanced computational tools show promise in elucidating complex interactions that occur between genes and environmental factors in diseases such as asthma; however appropriately designed studies are critical for these methods to reach their full potential. Objective: We used a case-control study to investigate whether genomic data (blood gene expression), viewed together with a spectrum of exposure effects and susceptibility markers (blood, urine and nail), can provide a mechanistic explanation for the increased susceptibility of asthmatics to ambient air pollutants. Methods: We studied 205 non-asthmatic and asthmatic children, (9-12 years of age) who participated in a clinical study in Detroit, Michigan. The study combines a traditional epidemiological design with an integrative approach to investigate the environmental exposure of children to indoor-outdoor air. The study includes measurements of internal dose (metals, allergen specific IgE, PAH and VOC metabolites) and clinical measures of health outcome (immunological, cardiovascular and respiratory). Results: Expected immunological indications of asthma have been obtained. In addition, initial results from our analyses point to the complex nature of childhood health and risk factors linked to metabolic syndrome (obesity, blood pressure and dyslipidemia). For example, 31% and 34% of the asthmatic MICA subjects were either overweight (BMI > 25) o

Wallerstein's World-Systems Analysis in Comparative Education: A Case Study

Science.gov (United States)

Griffiths, Tom G.; Knezevic, Lisa

2010-01-01

Since the 1970s, using his world-systems analysis, Immanuel Wallerstein has developed a wide-ranging framework for the social sciences, with potential applications for comparative educational research. In this paper we outline key aspects of Wallerstein's theorising, and then analyse the uptake, understandings, and applications of his analysis in…

Comparative analysis of catfish BAC end sequences with the zebrafish genome

Directory of Open Access Journals (Sweden)

Abernathy Jason

2009-12-01

Full Text Available Abstract Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3% had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5, of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.

Meditative Movement, Energetic, and Physical Analyses of Three Qigong Exercises: Unification of Eastern and Western Mechanistic Exercise Theory.

Science.gov (United States)

Klein, Penelope; Picard, George; Baumgarden, Joseph; Schneider, Roger

2017-09-23

Abstract : Qigong is the meditative movement and therapeutic exercise of Eastern medicine. A growing body of evidence is validating its health benefits leading to mechanistic questions of how it works. The purpose of this article is to explore mechanisms of action related to Qigong, with the intent of unifying Eastern and Western exercise theory and to present a model for Qigong exercise analysis. Three exercises from a standardized Qigong form: 'Plucking the Stars', 'Lotus Leaves Rustle in the Wind', and 'Pacing Forwards and Backwards' were selected for meditative, energetic, and physical analyses. Meditative aspects include relaxation response, interoception and exteroception. Energetic aspects include stimulation of meridians through mental intent, acupressure, and self-massage. Physical aspects include flexibility, strength, articular stimulation, neuro-integration, respiratory effect, fascial stretch, visceral massage, balance challenge CranioSacral pump, lymphatic and venous return and glandular stimulation, and physiologic response to relaxation. Knowledge of mechanisms of action for specific Qigong exercises can guide operational definition of Qigong, selection of outcomes assessment in future research, inform prescriptive practice addressing clinical health issues, and advance adoption of Qigong practice within integrative health care. The model of analysis demonstrated in this discussion may assist in these endeavors.

Phenomenological and mechanistic modeling of melt-structure-water interactions in a light water reactor severe accident

International Nuclear Information System (INIS)

Bui, V.A.

1998-01-01

The objective of this work is to address the modeling of the thermal hydrodynamic phenomena and interactions occurring during the progression of reactor severe accidents. Integrated phenomenological models are developed to describe the accident scenarios, which consist of many processes, while mechanistic modeling, including direct numerical simulation, is carried out to describe separate effects and selected physical phenomena of particular importance

Toward a Rational and Mechanistic Account of Mental Effort.

Science.gov (United States)

Shenhav, Amitai; Musslick, Sebastian; Lieder, Falk; Kool, Wouter; Griffiths, Thomas L; Cohen, Jonathan D; Botvinick, Matthew M

2017-07-25

In spite of its familiar phenomenology, the mechanistic basis for mental effort remains poorly understood. Although most researchers agree that mental effort is aversive and stems from limitations in our capacity to exercise cognitive control, it is unclear what gives rise to those limitations and why they result in an experience of control as costly. The presence of these control costs also raises further questions regarding how best to allocate mental effort to minimize those costs and maximize the attendant benefits. This review explores recent advances in computational modeling and empirical research aimed at addressing these questions at the level of psychological process and neural mechanism, examining both the limitations to mental effort exertion and how we manage those limited cognitive resources. We conclude by identifying remaining challenges for theoretical accounts of mental effort as well as possible applications of the available findings to understanding the causes of and potential solutions for apparent failures to exert the mental effort required of us.

Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2016-08-31

An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values.

Comparative genomic hybridization analysis of benign and invasive male breast neoplasms

DEFF Research Database (Denmark)

Ojopi, Elida Paula Benquique; Cavalli, Luciane Regina; Cavalieri, Luciane Mara Bogline

2002-01-01

Comparative genomic hybridization (CGH) analysis was performed for the identification of chromosomal imbalances in two benign gynecomastias and one malignant breast carcinoma derived from patients with male breast disease and compared with cytogenetic analysis in two of the three cases. CGH...... analysis demonstrated overrepresentation of 8q in all three cases. One case of gynecomastia presented gain of 1p34.3 through pter, 11p14 through q12, and 17p11.2 through qter, and loss of 1q41 through qter and 4q33 through qter. The other gynecomastia presented del(1)(q41) as detected by both cytogenetic...

Utilizing Mechanistic Cross-Linking Technology to Study Protein-Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab

Science.gov (United States)

Finzel, Kara; Beld, Joris; Burkart, Michael D.; Charkoudian, Louise K.

2017-01-01

Over the past decade, mechanistic cross-linking probes have been used to study protein-protein interactions in natural product biosynthetic pathways. This approach is highly interdisciplinary, combining elements of protein biochemistry, organic chemistry, and computational docking. Herein, we described the development of an experiment to engage…

Mechanistic approach for the kinetics of the decomposition of nitrous oxide over calcined hydrotalcites

Energy Technology Data Exchange (ETDEWEB)

Dandl, H.; Emig, G. [Lehrstuhl fuer Technische Chemie I, Erlangen (Germany)

1998-03-27

A highly active catalyst for the decomposition of N{sub 2}O was prepared by the thermal treatment of CoLaAl-hydrotalcite. For this catalyst the reaction rate was determined at various partial pressures of N{sub 2}O, O{sub 2} and H{sub 2}O in a temperature range from 573K to 823K. The kinetic simulation resulted in a mechanistic model. The energies of activation and rate coefficients are estimated for the main steps of the reaction

A Comparative Analysis of Charter Schools and Traditional Public Schools

Science.gov (United States)

Smith, Jodi Renee Abbott

2014-01-01

The focus of this descriptive research study was to compare charter and traditional public schools on the academic knowledge of fifth grade students as measured by Arizona's Instrument to Measure Standards (AIMS) in a suburb of a large southwestern city. This analysis also compared charter and traditional public schools on AYP status. It was…

Advantages of Wavelet analysis compared to Fourier analysis for the interpretation of electrochemical noise

International Nuclear Information System (INIS)

Espada, L.; Sanjurjo, M.; Urrejola, S.; Bouzada, F.; Rey, G.; Sanchez, A.

2003-01-01

Given its simplicity and low cost compared to other types of methodologies, the measurement and interpretation of Electrochemical Noise, is consolidating itself as one of the analysis methods most frequently used for the interpretation of corrosion. As the technique is still evolving, standard treatment methodologies for data retrieved in experiments do not exist yet. To date, statistical analysis and the Fourier analysis are commonly used in order to establish the parameters that may characterize the recording of potential and current electrochemical noise. This study introduces a new methodology based on wavelet analysis and presents its advantages with regards to the Fourier analysis in distinguishes periodical and non-periodical variations in the signal power in time and frequency, as opposed to the Fourier analysis that only considers the frequency. (Author) 15 refs

Alcohol: view 2000 - comparative analysis gasoline versus alcohol

International Nuclear Information System (INIS)

Rocha, P.G. da; Vasconcelos, C.R. de

1990-01-01

The comparative analysis between alcohol and gas reveals the pros and the cons of the use of each one of those energy sources, taking as a basis an analysis of the world supply and demand of oil, and of PETROBRAS sceneries, including price expectancies for next decade, and the repercussion of PROALCOOL during its existence in the country. Regarding competitiveness, gas and the energy substitute hydrous alcohol are analyzed jointly, as an energy policy for carburetant fuels, taking into account aspects related with both the direct and the indirect cost of each energy source, as well as the benefits provided by then both. (author)

Mechanistic Studies of Hafnium-Pyridyl Amido-Catalyzed 1-Octene Polymerization and Chain Transfer Using Quench-Labeling Methods.

Science.gov (United States)

Cueny, Eric S; Johnson, Heather C; Anding, Bernie J; Landis, Clark R

2017-08-30

Chromophore quench-labeling applied to 1-octene polymerization as catalyzed by hafnium-pyridyl amido precursors enables quantification of the amount of active catalyst and observation of the molecular weight distribution (MWD) of Hf-bound polymers via UV-GPC analysis. Comparison of the UV-detected MWD with the MWD of the "bulk" (all polymers, from RI-GPC analysis) provides important mechanistic information. The time evolution of the dual-detection GPC data, concentration of active catalyst, and monomer consumption suggests optimal activation conditions for the Hf pre-catalyst in the presence of the activator [Ph 3 C][B(C 6 F 5 ) 4 ]. The chromophore quench-labeling agents do not react with the chain-transfer agent ZnEt 2 under the reaction conditions. Thus, Hf-bound polymeryls are selectively labeled in the presence of zinc-polymeryls. Quench-labeling studies in the presence of ZnEt 2 reveal that ZnEt 2 does not influence the rate of propagation at the Hf center, and chain transfer of Hf-bound polymers to ZnEt 2 is fast and quasi-irreversible. The quench-label techniques represent a means to study commercial polymerization catalysts that operate with high efficiency at low catalyst concentrations without the need for specialized equipment.

Comparative genome analysis of Basidiomycete fungi

Energy Technology Data Exchange (ETDEWEB)

Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

2013-08-07

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

In Vitro–In Vivo Correlation for Gliclazide Immediate-Release Tablets Based on Mechanistic Absorption Simulation

OpenAIRE

Grbic, Sandra; Parojcic, Jelena; Ibric, Svetlana; Djuric, Zorica

2010-01-01

The aim of this study was to develop a drug-specific absorption model for gliclazide (GLK) using mechanistic gastrointestinal simulation technology (GIST) implemented in GastroPlusTM software package. A range of experimentally determined, in silico predicted or literature data were used as input parameters. Experimentally determined pH-solubility profile was used for all simulations. The human jejunum effective permeability (Peff) value was estimated on the basis of in vitro measured Caco-2 p...

IMG: the integrated microbial genomes database and comparative analysis system

Science.gov (United States)

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

2012-01-01

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

Epithelial apoptosis in mechanistically distinct methods of injury in the murine small intestine

Science.gov (United States)

Vyas, Dinesh; Robertson, Charles M; Stromberg, Paul E; Martin, James R.; Dunne, W. Michael; Houchen, Courtney W; Barrett, Terrence A; Ayala, Alfred; Perl, Mario; Buchman, Timothy G; Coopersmith, Craig M

2007-01-01

Gut epithelial apoptosis is involved in the pathophysiology of multiple diseases. This study characterized intestinal apoptosis in three mechanistically distinct injuries with different kinetics of cell death. FVB/N mice were subjected to gamma radiation, Pseudomonas aeruginosa pneumonia or injection of monoclonal anti-CD3 antibody and sacrificed 4, 12, or 24 hours post-injury (n=10/time point). Apoptosis was quantified in the jejunum by hematoxylin and eosin (H&E), active caspase-3, terminal deoxynucleotidyl transferase dUTP-mediated nick end labeling (TUNEL), in situ oligoligation reaction (ISOL,) cytokeratin 18, and annexin V staining. Reproducible results were obtained only for H&E, active caspase-3, TUNEL and ISOL, which were quantified and compared against each other for each injury at each time point. Kinetics of injury were different with early apoptosis highest following radiation, late apoptosis highest following anti CD3, and more consistent levels following pneumonia. ISOL was the most consistent stain and was always statistically indistinguishable from at least 2 stains. In contrast, active caspase-3 demonstrated lower levels of apoptosis, while the TUNEL assay had higher levels of apoptosis in the most severely injured intestine regardless of mechanism of injury. H&E was a statistical outlier more commonly than any other stain. This suggests that regardless of mechanism or kinetics of injury, ISOL correlates to other quantification methods of detecting gut epithelial apoptosis more than any other method studied and compares favorably to other commonly accepted techniques of quantifying apoptosis in a large intestinal cross sectional by balancing sensitivity and specificity across a range of times and levels of death. PMID:17357092

The kinetic and mechanistic aspects of the oxidative dehydrogenation of ethane over Li/Na/MgO catalysts

NARCIS (Netherlands)

Swaan, H.M.; Swaan, H.M.; Toebes, A.; Toebes, A.; van Ommen, J.G.; Seshan, Kulathuiyer; Ross, J.R.H.; Ross, J.R.H.

1992-01-01

Kinetic and mechanistic aspects of the oxidative dehydrogenation of ethane catalysed by Li/MgO and Li/Na/MgO have been investigated. Initial rate measurements at 600°C; revealed that the Li/MgO catalyst produced C2H4, CO2, CO and H2 by parallel reactions whereas the sodium-promoted catalyst produced

Phenomenological and mechanistic modeling of melt-structure-water interactions in a light water reactor severe accident

Energy Technology Data Exchange (ETDEWEB)

Bui, V.A

1998-10-01

The objective of this work is to address the modeling of the thermal hydrodynamic phenomena and interactions occurring during the progression of reactor severe accidents. Integrated phenomenological models are developed to describe the accident scenarios, which consist of many processes, while mechanistic modeling, including direct numerical simulation, is carried out to describe separate effects and selected physical phenomena of particular importance 88 refs, 54 figs, 7 tabs

Mechanistic analysis of solute transport in an in vitro physiological two-phase dissolution apparatus.

Science.gov (United States)

Mudie, Deanna M; Shi, Yi; Ping, Haili; Gao, Ping; Amidon, Gordon L; Amidon, Gregory E

2012-10-01

In vitro dissolution methodologies that adequately capture the oral bioperformance of solid dosage forms are critical tools needed to aid formulation development. Such methodologies must encompass important physiological parameters and be designed with drug properties in mind. Two-phase dissolution apparatuses, which contain an aqueous phase in which the drug dissolves (representing the dissolution/solubility component) and an organic phase into which the drug partitions (representing the absorption component), have the potential to provide meaningful predictions of in vivo oral bioperformance for some BCS II, and possibly some BCS IV drug products. Before such an apparatus can be evaluated properly, it is important to understand the kinetics of drug substance partitioning from the aqueous to the organic medium. A mass transport analysis was performed of the kinetics of partitioning of drug substance solutions from the aqueous to the organic phase of a two-phase dissolution apparatus. Major assumptions include pseudo-steady-state conditions, a dilute aqueous solution and diffusion-controlled transport. Input parameters can be measured or estimated a priori. This paper presents the theory and derivation of our analysis, compares it with a recent kinetic approach, and demonstrates its effectiveness in predicting in vitro partitioning profiles of three BCS II weak acids in four different in vitro two-phase dissolution apparatuses. Very importantly, the paper discusses how a two-phase apparatus can be scaled to reflect in vivo absorption kinetics and for which drug substances the two-phase dissolution systems may be appropriate tools for measuring oral bioperformance. Copyright © 2012 John Wiley & Sons, Ltd.

Mechanistic insights into the use of oxide nanoparticles coated asymmetric electrodes for capacitive deionization

International Nuclear Information System (INIS)

Han, Linchen; Karthikeyan, K.G.; Anderson, M.A.; Wouters, J.J.; Gregory, Kelvin B.

2013-01-01

Highlights: ► Capacitive deionization is an emerging, low-pressure desalination method that can compete with the current mainstream technologies. ► Novel electrode materials (i.e., porous conducting carbon modified with non-conducting oxides applied as nanoporous (NP) films) were tested. ► The NP-oxide coatings increased the sorption capacity and process efficiency by shifting the working potential to a higher efficiency range. ► Experimental data were described using both mechanistic and empirical models to elucidate underlying process mechanisms. ► Our results are expected to facilitate future CDI system design and development of appropriate electrode materials. -- Abstract: Capacitive deionization (CDI) is an emerging water desalination method, which employs high surface area porous electrode materials for electro-sorption of ions. We used an asymmetric CDI cell constructed with alumina and silica nanoparticle (NP) coated electrodes and KCl as a probe electrolyte to gain insights into electro-sorption behavior and elucidate underlying process mechanisms. This CDI system is efficient for use in desalination and up to 15 to 60 μmol/g (total electrode) sorption capacity was achieved. Higher removal of K + compared to Cl − was obtained attributable to competition between OH − and Cl − . The presence of NPs not only creates highly accessible surface area but also increases the charge efficiency by shifting the applied potential to a high efficiency range due to protonation/deprotonation occurring on metal oxide surfaces. Data were described using both mechanistic electrical double layer (EDL) based Gouy–Chapman–Stern (GCS) formulation and empirical Freundlich equations. Our results suggest that the presence of metal oxide NPs can effectively modify the isoelectric points and an increase in planar charge efficiency of up to 20% could be achieved. However, global charge efficiency was still severely constrained by backward thermal diffusion and

a comparative analysis of first day neonatal mortality between

African Journals Online (AJOL)

East African Medical Journal Vol. 90 No. 11 November 2013. A COMPARATIVE ANALYSIS OF FIRST DAY NEONATAL MORTALITY BETWEEN ADOLESCENTS AND ADULT. FEMALES GIVING BIRTH AT LIGULA HOSPITAL IN MTWARA, SOUTH EASTERN TANZANIA 2008 – 2009. A. Ramaiya, MSc, Ifakara Health ...

Mechanistic Drifting Forecast Model for A Small Semi-Submersible Drifter Under Tide-Wind-Wave Conditions

Science.gov (United States)

Zhang, Wei-Na; Huang, Hui-ming; Wang, Yi-gang; Chen, Da-ke; Zhang, lin

2018-03-01

Understanding the drifting motion of a small semi-submersible drifter is of vital importance regarding monitoring surface currents and the floating pollutants in coastal regions. This work addresses this issue by establishing a mechanistic drifting forecast model based on kinetic analysis. Taking tide-wind-wave into consideration, the forecast model is validated against in situ drifting experiment in the Radial Sand Ridges. Model results show good performance with respect to the measured drifting features, characterized by migrating back and forth twice a day with daily downwind displacements. Trajectory models are used to evaluate the influence of the individual hydrodynamic forcing. The tidal current is the fundamental dynamic condition in the Radial Sand Ridges and has the greatest impact on the drifting distance. However, it loses its leading position in the field of the daily displacement of the used drifter. The simulations reveal that different hydrodynamic forces dominate the daily displacement of the used drifter at different wind scales. The wave-induced mass transport has the greatest influence on the daily displacement at Beaufort wind scale 5-6; while wind drag contributes mostly at wind scale 2-4.

Iterative Systems Biology for Medicine – time for advancing from network signature to mechanistic equations

KAUST Repository

Gomez-Cabrero, David

2017-05-09

The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of systems biology arduous. However, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

Mechanistic model coupling gas exchange dynamics and Listeria monocytogenes growth in modified atmosphere packaging of non respiring food.

Science.gov (United States)

Chaix, E; Broyart, B; Couvert, O; Guillaume, C; Gontard, N; Guillard, V

2015-10-01

A mechanistic model coupling O2 and CO2 mass transfer (namely diffusion and solubilisation in the food itself and permeation through the packaging material) to microbial growth models was developed aiming at predicting the shelf life of modified atmosphere packaging (MAP) systems. It was experimentally validated on a non-respiring food by investigating concomitantly the O2/CO2 partial pressure in packaging headspace and the growth of Listeria monocytogenes (average microbial count) within the food sample. A sensitivity analysis has revealed that the reliability of the prediction by this "super-parametrized" model (no less than 47 parameters were required for running one simulation) was strongly dependent on the accuracy of the microbial input parameters. Once validated, this model was used to decipher the role of O2/CO2 mass transfer on microbial growth and as a MAP design tool: an example of MAP dimensioning was provided in this paper as a proof of concept. Copyright © 2015 Elsevier Ltd. All rights reserved.

Confinement effects and mechanistic aspects for montmorillonite nanopores.

Science.gov (United States)

Li, Xiong; Zhu, Chang; Jia, Zengqiang; Yang, Gang

2018-08-01

Owing to the ubiquity, critical importance and special properties, confined microenvironments have recently triggered overwhelming interest. In this work, all-atom molecular dynamics simulations have been conducted to address the confinement effects and ion-specific effects for electrolyte solutions within montmorillonite nanopores, where the pore widths vary with a wide range. The adsorption number, structure, dynamics and stability of inner- and outer-sphere metal ions are affected by the change of pore widths (confinement effects), while the extents are significantly dependent on the type of adsorbed species. The type of adsorbed species is, however, not altered by the magnitude of confinement effects, and confinement effects are similar for different electrolyte concentrations. Ion-specific effects are pronounced for all magnitudes of confinement effects (from non- to strong confined conditions), and Hofmeister sequences of outer-sphere species are closely associated with the magnitude of confinement effects while those of inner-sphere species remain consistent. In addition, mechanistic aspects of confinement have been posed using the electrical double layer theories, and the results can be generalized to other confined systems that are ubiquitous in biology, chemistry, geology and nanotechnology. Copyright © 2018 Elsevier Inc. All rights reserved.

Unraveling molecular mechanistic differences in liver metabolism between lean and fat lines of Pekin duck (Anas platyrhynchos domestica): a proteomic study.

Science.gov (United States)

Zheng, Aijuan; Chang, Wenhuan; Hou, Shuisheng; Zhang, Shu; Cai, Huiyi; Chen, Guilan; Lou, Ruiying; Liu, Guohua

2014-02-26

Duck is one of the major poultry meat sources for human consumption. To satisfy different eating habits, lean and fat strains of Pekin ducks have been developed. The objective of this study was to determine the molecular mechanistic differences in liver metabolism between two duck strains. The liver proteome of the Pekin duck lines was compared on days 1, 14, 28, and 42 posthatching using 2-DE based proteomics. There was a different abundance of 76 proteins in the livers of the two duck lines. Fat ducks strongly expressed proteins related to pathways of glycolysis, ATP synthesis, and protein catabolism, suggesting enhanced fat deposition rather than protein retention. In contrast, highly expressed proteins in lean ducks improved protein anabolism and reduced protein catabolism, resulting in an enhancement of lean meat deposition. Along with the decrease in fat deposition, the immune system of the lean duck strain may be enhanced by enhanced expression of proteins involved in stress response, immune defense, and antioxidant functions. These results indicate that selection pressure has shaped the two duck lines differently resulting in different liver metabolic capacities. These observed variations between the two strains at the molecular level are matched with physiological changes in growth performance and meat production. This information may have beneficial impacts in areas such as genetic modification through the manipulation of target proteins or genes in specific pathways to improve the efficiency of duck meat production. The objective of this study was to unravel molecular mechanistic differences in liver metabolism between lean and fat Pekin duck (Anas platyrhynchos domestica) strains. There was a different abundance of 76 proteins in the livers of the two duck lines. Enhanced protein expression in the fat ducks related to pathways of glycolysis, ATP synthesis and protein catabolism suggesting increased fat deposition rather than protein retention. In

Characterization of cementitiously stabilized subgrades for mechanistic-empirical pavement design

Science.gov (United States)

Solanki, Pranshoo

Pavements are vulnerable to subgrade layer performance because it acts as a foundation. Due to increase in the truck traffic, pavement engineers are challenged to build more strong and long-lasting pavements. To increase the load-bearing capacity of pavements, subgrade layer is often stabilized with cementitious additives. Thus, an overall characterization of stabilized subgrade layer is important for enhanced short- and long-term pavement performance. In this study, the effect of type and amount of additive on the short-term performance in terms of material properties recommended by the new Mechanistic-Empirical Pavement Design Guide (MEPDG) is examined. A total of four soils commonly encountered as subgrades in Oklahoma are utilized. Results show that the changes in the Mr, ME and UCS values stabilized specimens depend on the soil type and properties of additives. The long-term performance (or durability) of stabilized soil specimens is investigated by conducting freeze-thaw (F-T) cycling, vacuum saturation and tube suction tests on 7-day cured P-, K- and C-soil specimens stabilized with 6% lime, 10% CFA and 10% CKD. This study is motivated by the fact that during the service life of pavement stabilized layers are subjected to F-T cycles and moisture variations. It is found that that UCS value of all the stabilized specimens decreased with increase in the number of F-T cycles. A strong correlation was observed between UCS values retained after vacuum saturation and F-T cycles indicating that vacuum saturation could be used as a time-efficient and inexpensive method for evaluating durability of stabilized soils. In this study, short- and long-term observations from stabilization of sulfate bearing soil with locally available low (CFA), moderate (CKD) and high (lime) calcium-based stabilizers are determined to evaluate and compare the effect of additive type on the phenomenon of sulfate-induced heave. The impact of different factors on the development of the

An experimental-numerical method for comparative analysis of joint prosthesis

International Nuclear Information System (INIS)

Claramunt, R.; Rincon, E.; Zubizarreta, V.; Ros, A.

2001-01-01

The difficulty that exists in the analysis of mechanical stresses in bones is high due to its complex mechanical and morphological characteristics. This complexity makes generalists modelling and conclusions derived from prototype tests very questionable. In this article a relatively simple comparative analysis systematic method that allow us to establish some behaviour differences in different kind of prosthesis is presented. The method, applicable in principle to any joint problem, is based on analysing perturbations produced in natural stress states of a bone after insertion of a joint prosthesis and combines numerical analysis using a 3-D finite element model and experimental studies based on photoelastic coating and electric extensometry. The experimental method is applied to compare two total hip prosthesis cement-free femoral stems of different philosophy. One anatomic of new generation, being of oblique setting over cancellous bone and the other madreporique of trochantero-diaphyseal support over cortical bone. (Author) 4 refs

Comparative analysis of transformed potato microtubers and its non ...

African Journals Online (AJOL)

The rapid progress of transgenic biotechnology has significantly promoted the development and production of genetically modified (GM) crops. The aim of this study was to compare some compositional analysis and genetic variation of transformed potato microtubers (Solanum tuberosum L. Desiree) line (which harbor ...

Comparative analysis of minor histocompatibility antigens genotyping methods

Directory of Open Access Journals (Sweden)

A. S. Vdovin

2016-01-01

Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.

Isolation, characterization, and mechanistic studies of (-)-alpha-gurjunene synthase from Solidago canadensis.

Science.gov (United States)

Schmidt, C O; Bouwmeester, H J; Bülow, N; König, W A

1999-04-15

The leaves of the composite Solidago canadensis (goldenrod) were shown to contain (-)-alpha-gurjunene synthase activity. This sesquiterpene is likely to be the precursor for cyclocolorenone, a sesquiterpene ketone present in high amounts in S. canadensis leaves. (-)-alpha-Gurjunene synthase was purified to apparent homogeneity (741-fold) by anion-exchange chromatography (on several matrices), dye ligand chromatography, hydroxylapatite chromatography, and gel filtration. Chromatography on a gel filtration matrix indicated a native molecular mass of 48 kDa, and SDS-PAGE showed the enzyme to be composed of one subunit with a denatured mass of 60 kDa. Its maximum activity was observed at pH 7.8 in the presence of 10 mM Mg2+ and the KM value for the substrate farnesyl diphosphate was 5.5 microM. Over a range of purification steps (-)-alpha-gurjunene and (+)-gamma-gurjunene synthase activities copurified. In addition, the product ratio of the enzyme activity under several different assay conditions was always 91% (-)-alpha-gurjunene and 9% (+)-gamma-gurjunene. This suggests that the formation of these two structurally related products is catalyzed by one enzyme. For further confirmation, we carried out a number of mechanistic studies with (-)-alpha-gurjunene synthase, in which an enzyme preparation was incubated with deuterated substrate analogues. Based on mass spectrometry analysis of the products formed, a cyclization mechanism was postulated which makes it plausible that the synthase catalyzes the formation of both sesquiterpenes. Copyright 1999 Academic Press.

Reliability on intra-laboratory and inter-laboratory data of hair mineral analysis comparing with blood analysis.

Science.gov (United States)

Namkoong, Sun; Hong, Seung Phil; Kim, Myung Hwa; Park, Byung Cheol

2013-02-01

Nowadays, although its clinical value remains controversial institutions utilize hair mineral analysis. Arguments about the reliability of hair mineral analysis persist, and there have been evaluations of commercial laboratories performing hair mineral analysis. The objective of this study was to assess the reliability of intra-laboratory and inter-laboratory data at three commercial laboratories conducting hair mineral analysis, compared to serum mineral analysis. Two divided hair samples taken from near the scalp were submitted for analysis at the same time, to all laboratories, from one healthy volunteer. Each laboratory sent a report consisting of quantitative results and their interpretation of health implications. Differences among intra-laboratory and interlaboratory data were analyzed using SPSS version 12.0 (SPSS Inc., USA). All the laboratories used identical methods for quantitative analysis, and they generated consistent numerical results according to Friedman analysis of variance. However, the normal reference ranges of each laboratory varied. As such, each laboratory interpreted the patient's health differently. On intra-laboratory data, Wilcoxon analysis suggested they generated relatively coherent data, but laboratory B could not in one element, so its reliability was doubtful. In comparison with the blood test, laboratory C generated identical results, but not laboratory A and B. Hair mineral analysis has its limitations, considering the reliability of inter and intra laboratory analysis comparing with blood analysis. As such, clinicians should be cautious when applying hair mineral analysis as an ancillary tool. Each laboratory included in this study requires continuous refinement from now on for inducing standardized normal reference levels.

Towards the development of mechanistically based design rules for corrosion fatigue in ductile steels

International Nuclear Information System (INIS)

Johnson, R.; McMinn, A.; Tomkins, B.

1980-08-01

Design curves for nuclear pressure vessels and off-shore structures are based on air endurance curves that have had a safety factor applied to account for effects such as corrosive environments, frequency and mean stress. These are supported by a limited number of endurance tests on actual pressure vessels, and on welded joints under service conditions. These data-based rules are limited in their ability to cope with environmental effects and as the time dependencies of fatigue and corrosion processes are so different, no sound basis exists for the extrapolation of data to long component lifetimes. The crack-growth behaviour of materials used in nuclear pressure vessels and off-shore structures is examined with a view to determining how it may be used to re-assess the design curves. Even simple integration of crack-growth laws can be seen to be within reasonable agreement with present design curves; with improved methods of stress analysis, etc. this approach could potentially improve these curves. Mechanistic studies are also seen to offer a means of examining and assessing time-dependent process interactions and so, potentially, to form the basis of new guidelines. Finally the areas where further work would be needed to substantiate any changes in design curves are indicated. (author)

A Comparative Analysis of Wiki Discretionary Access Control in a CONOPS Environment

National Research Council Canada - National Science Library

Crawford, Frederick L

2008-01-01

This research conducts a comparative analysis of discretionary access controls of current wikis by experimenting with their discretionary access controls and functionality, comparing the wiki software...

Discrimination based on HIV/AIDS status: A comparative analysis of ...

African Journals Online (AJOL)

Discrimination based on HIV/AIDS status: A comparative analysis of the Nigerian court's decision in Festus Odaife & Ors v Attorney General of the Federation & Ors with other Commonwealth jurisdictions.

COMPARATIVE ANALYSIS OF TRANSPORT AIRCRAFT, BACKROUND FOR SHORT/ MEDIUM COURIER TRANSPORT AIRCRAFT PROCUREMENT

Directory of Open Access Journals (Sweden)

Matei POPA

2010-03-01

Full Text Available In accordance with Air Force requirements, the comparative analysis of short/medium transport aircraft comes to sustain procurement decision of short/medium transport aircraft. This paper presents, in short, the principles and the results of the comparative analysis for short/medium military transport aircraft.

Assessing first-order emulator inference for physical parameters in nonlinear mechanistic models

Science.gov (United States)

Hooten, Mevin B.; Leeds, William B.; Fiechter, Jerome; Wikle, Christopher K.

2011-01-01

We present an approach for estimating physical parameters in nonlinear models that relies on an approximation to the mechanistic model itself for computational efficiency. The proposed methodology is validated and applied in two different modeling scenarios: (a) Simulation and (b) lower trophic level ocean ecosystem model. The approach we develop relies on the ability to predict right singular vectors (resulting from a decomposition of computer model experimental output) based on the computer model input and an experimental set of parameters. Critically, we model the right singular vectors in terms of the model parameters via a nonlinear statistical model. Specifically, we focus our attention on first-order models of these right singular vectors rather than the second-order (covariance) structure.

Weight of evidence analysis for assessing the genotoxic potential of carbon nanotubes

DEFF Research Database (Denmark)

Møller, Peter; Jacobsen, Nicklas Raun

2017-01-01

Carbon nanotube (CNT) is a nanomaterial that has received interest because of its high-tensile strength and low weight. Although CNTs differ substantially in physico-chemical properties, they share high aspect ratio which resembles that of asbestos and other fibers causing lung cancer...... and insufficient mechanistic evidence. Damage to DNA is considered to be a key mechanistic step in the development of fiber-induced cancer. Thus, the genotoxic potential can be a cornerstone in the evaluation of hazards of CNTs. The present study used a weight of evidence (WoE) analysis to evaluate...

Improving the prediction of methane production and representation of rumen fermentation for finishing beef cattle within a mechanistic model

NARCIS (Netherlands)

Ellis, J.L.; Dijkstra, J.; Bannink, A.; Kebreab, E.; Archibeque, S.; Benchaar, C.; Beauchemin, K.; Nkrumah, D.J.; France, J.

2014-01-01

The purpose of this study was to evaluate prediction of methane emissions from finishing beef cattle using an extant mechanistic model with pH-independent or pH-dependent VFA stoichiometries, a recent stoichiometry adjustment for the use of monensin, and adaptation of the underlying model structure,

Comparative Analysis of Students’ Media Competences Levels

Directory of Open Access Journals (Sweden)

Alexander Fedorov

2015-08-01

Full Text Available This article analyzed the results of survey of university students’ media literacy competence (on the base of a classification of indicators of media literacy competence of the audience as an effective tool for comparative analysis of the levels of development of media competence of students of the control and experimental groups: the level of media competence of students who have a one-year training course in the framework of media literacy education courses four times higher than in similar indicators in the control group. Analysis of the results of this survey confirmed the general trend of media contacts of student audience – its orientation to entertainment genres of audiovisual media, visually appealing; positive, active, unmarried, childless, educated, highly qualified characters (primarily – male characters aged 19 to 35 years. These heroes are characteristic optimism, independence, intelligence, emotion. They have an excellent command of the life situation and have a positive impact on the development progress of the plot of a media text.

Toward a mechanistic modeling of nitrogen limitation on vegetation dynamics.

Science.gov (United States)

Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D; Wilson, Cathy J; Cai, Michael; McDowell, Nate G

2012-01-01

Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO(2) concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO(2) concentration, temperature, and radiation when evaluated against published data of V(c,max) (maximum carboxylation rate) and J(max) (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO(2) concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions and the vegetation

Toward a Mechanistic Modeling of Nitrogen Limitation on Vegetation Dynamics

Science.gov (United States)

Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D.; Wilson, Cathy J.; Cai, Michael; McDowell, Nate G.

2012-01-01

Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO2 concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO2 concentration, temperature, and radiation when evaluated against published data of Vc,max (maximum carboxylation rate) and Jmax (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO2 concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions and the vegetation feedbacks

Toward a mechanistic modeling of nitrogen limitation on vegetation dynamics.

Directory of Open Access Journals (Sweden)

Chonggang Xu

Full Text Available Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO(2 concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO(2 concentration, temperature, and radiation when evaluated against published data of V(c,max (maximum carboxylation rate and J(max (maximum electron transport rate. A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO(2 concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions and the

Experimental validation for combustion analysis of GOTHIC code in 2-dimensional combustion chamber

International Nuclear Information System (INIS)

Lee, J. W.; Yang, S. Y.; Park, K. C.; Jung, S. H.

2002-01-01

In this study, the prediction capability of GOTHIC code for hydrogen combustion phenomena was validated with the results of two-dimensional premixed hydrogen combustion experiment executed by Seoul National University. The experimental chamber has about 24 liter free volume (1x0.024x1 m 3 ) and 2-dimensional rectangular shape. The test were preformed with 10% hydrogen/air gas mixture and conducted with combination of two igniter positions (top center, top corner) and two boundary conditions (bottom full open, bottom right half open). Using the lumped parameter and mechanistic combustion model in GOTHIC code, the SNU experiments were simulated under the same conditions. The GOTHIC code prediction of the hydrogen combustion phenomena did not compare well with the experimental results. In case of lumped parameter simulation, the combustion time was predicted appropriately. But any other local information related combustion phenomena could not be obtained. In case of mechanistic combustion analysis, the physical combustion phenomena of gas mixture were not matched experimental ones. In boundary open cases, the GOTHIC predicted very long combustion time and the flame front propagation could not simulate appropriately. Though GOTHIC showed flame propagation phenomenon in adiabatic calculation, the induction time of combustion was still very long compare with experimental results. Also, it was found that the combustion model of GOTHIC code had some weak points in low concentration of hydrogen combustion simulation

Life at the Common Denominator: Mechanistic and Quantitative Biology for the Earth and Space Sciences

Science.gov (United States)

Hoehler, Tori M.

2010-01-01

The remarkable challenges and possibilities of the coming few decades will compel the biogeochemical and astrobiological sciences to characterize the interactions between biology and its environment in a fundamental, mechanistic, and quantitative fashion. The clear need for integrative and scalable biology-environment models is exemplified in the Earth sciences by the challenge of effectively addressing anthropogenic global change, and in the space sciences by the challenge of mounting a well-constrained yet sufficiently adaptive and inclusive search for life beyond Earth. Our understanding of the life-planet interaction is still, however, largely empirical. A variety of approaches seek to move from empirical to mechanistic descriptions. One approach focuses on the relationship between biology and energy, which is at once universal (all life requires energy), unique (life manages energy flow in a fashion not seen in abiotic systems), and amenable to characterization and quantification in thermodynamic terms. Simultaneously, a focus on energy flow addresses a critical point of interface between life and its geological, chemical, and physical environment. Characterizing and quantifying this relationship for life on Earth will support the development of integrative and predictive models for biology-environment dynamics. Understanding this relationship at its most fundamental level holds potential for developing concepts of habitability and biosignatures that can optimize astrobiological exploration strategies and are extensible to all life.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Directory of Open Access Journals (Sweden)

Moreau Yves

2005-05-01

Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

Comparative Life-Cycle Cost Analysis Of Solar Photovoltaic Power ...

African Journals Online (AJOL)

Comparative Life-Cycle Cost Analysis Of Solar Photovoltaic Power System And Diesel Generator System For Remote Residential Application In Nigeria. ... like capital cost, and diesel fuel costs are varied. The results show the photovoltaic system to be more cost-effective at low-power ranges of electrical energy supply.

Comparative analysis of solid waste management in 20 cities

NARCIS (Netherlands)

Wilson, D.C.; Rodic-Wiersma, L.; Scheinberg, A.; Velis, C.A.; Alabaster, G.

2012-01-01

This paper uses the ‘lens’ of integrated and sustainable waste management (ISWM) to analyse the new data set compiled on 20 cities in six continents for the UN-Habitat flagship publication Solid Waste Management in the World’s Cities. The comparative analysis looks first at waste generation rates

Mechanistic modeling of aberrant energy metabolism in human disease

Directory of Open Access Journals (Sweden)

Vineet eSangar

2012-10-01

Full Text Available Dysfunction in energy metabolism—including in pathways localized to the mitochondria—has been implicated in the pathogenesis of a wide array of disorders, ranging from cancer to neurodegenerative diseases to type II diabetes. The inherent complexities of energy and mitochondrial metabolism present a significant obstacle in the effort to understand the role that these molecular processes play in the development of disease. To help unravel these complexities, systems biology methods have been applied to develop an array of computational metabolic models, ranging from mitochondria-specific processes to genome-scale cellular networks. These constraint-based models can efficiently simulate aspects of normal and aberrant metabolism in various genetic and environmental conditions. Development of these models leverages—and also provides a powerful means to integrate and interpret—information from a wide range of sources including genomics, proteomics, metabolomics, and enzyme kinetics. Here, we review a variety of mechanistic modeling studies that explore metabolic functions, deficiency disorders, and aberrant biochemical pathways in mitochondria and related regions in the cell.

Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse.

Science.gov (United States)

Agarwal, Vinayak; Miles, Zachary D; Winter, Jaclyn M; Eustáquio, Alessandra S; El Gamal, Abrahim A; Moore, Bradley S

2017-04-26

Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.

Comparative analysis of evaluation techniques for transport policies

International Nuclear Information System (INIS)

Browne, David; Ryan, Lisa

2011-01-01

The objective of this paper is to examine and compare the use of a number of policy evaluation tools, which can be used to measure the impact of transport policies and programmes as part of a strategic environmental assessment (SEA) or sustainability appraisal. The evaluation tools that were examined include cost-benefit analysis (CBA), cost-effectiveness analysis (CEA) and multi-criteria decision analysis (MCDA). It was concluded that both CEA and CBA are useful for estimating the costs and/or benefits associated with transport policies but are constrained by the difficulty in quantifying non-market impacts and monetising total costs and benefits. Furthermore, CEA is limited to identifying the most 'cost-effective policy' for achieving a single, narrowly defined objective, usually greenhouse gas (GHG) reduction and is, therefore, not suitable for evaluating policy options with ancillary costs or a variety of potential benefits. Thus, CBA or CEA evaluation should be complemented by a complete environmental and socio-economic impact assessment approach such as MCDA. This method allows for participatory analysis and qualitative assessment but is subject to caveats such as subjectivity and value-laden judgments.

Fire in the Plio-Pleistocene: the functions of hominin fire use, and the mechanistic, developmental and evolutionary consequences.

Science.gov (United States)

Attwell, Laura; Kovarovic, Kris; Kendal, Jeremy

2015-07-20

Fire is a powerful natural force that can change landscapes extremely quickly. Hominins have harnessed this resource for their own purposes, with mechanistic and developmental physiological consequences. In addition, the use of fire has niche constructive effects, altering selective environments for genetic and cultural evolution. We review the record for hominin fire use in the Plio-Pleistocene, before considering the various functions for its use, and the resultant mechanistic and developmental consequences. We also adopt the niche construction framework to consider how the use of fire can modify selective environments, and thus have evolutionary consequences at genetic and cultural levels. The light that fire produces may influence photoperiodicity and alter hormonally-controlled bodily rhythms. Fire used for cooking could have extended the range of foods hominins were able to consume, and reduced digestion costs. This may have contributed to the expansion of the hominin brain and facial anatomy, influenced by a higher quality cooked diet. Fire may also have allowed dispersal into northern areas with much cooler climates than the hominin African origin, posing novel problems that affected diet and social behaviour.

Comparative analysis of clustering methods for gene expression time course data

Directory of Open Access Journals (Sweden)

Ivan G. Costa

2004-01-01

Full Text Available This work performs a data driven comparative study of clustering methods used in the analysis of gene expression time courses (or time series. Five clustering methods found in the literature of gene expression analysis are compared: agglomerative hierarchical clustering, CLICK, dynamical clustering, k-means and self-organizing maps. In order to evaluate the methods, a k-fold cross-validation procedure adapted to unsupervised methods is applied. The accuracy of the results is assessed by the comparison of the partitions obtained in these experiments with gene annotation, such as protein function and series classification.

Comparing Visual and Statistical Analysis of Multiple Baseline Design Graphs.

Science.gov (United States)

Wolfe, Katie; Dickenson, Tammiee S; Miller, Bridget; McGrath, Kathleen V

2018-04-01

A growing number of statistical analyses are being developed for single-case research. One important factor in evaluating these methods is the extent to which each corresponds to visual analysis. Few studies have compared statistical and visual analysis, and information about more recently developed statistics is scarce. Therefore, our purpose was to evaluate the agreement between visual analysis and four statistical analyses: improvement rate difference (IRD); Tau-U; Hedges, Pustejovsky, Shadish (HPS) effect size; and between-case standardized mean difference (BC-SMD). Results indicate that IRD and BC-SMD had the strongest overall agreement with visual analysis. Although Tau-U had strong agreement with visual analysis on raw values, it had poorer agreement when those values were dichotomized to represent the presence or absence of a functional relation. Overall, visual analysis appeared to be more conservative than statistical analysis, but further research is needed to evaluate the nature of these disagreements.

Comparative analysis of time efficiency and spatial resolution between different EIT reconstruction algorithms

International Nuclear Information System (INIS)

Kacarska, Marija; Loskovska, Suzana

2002-01-01

In this paper comparative analysis between different EIT algorithms is presented. Analysis is made for spatial and temporal resolution of obtained images by several different algorithms. Discussions consider spatial resolution dependent on data acquisition method, too. Obtained results show that conventional applied-current EIT is more powerful compared to induced-current EIT. (Author)

Mechanistic target of rapamycin (MTOR) protein expression in the tumor and its microenvironment correlates with more aggressive pathology at cystectomy

NARCIS (Netherlands)

Winters, B.R. (Brian R.); Vakar-Lopez, F. (Funda); Brown, L. (Lisha); Montgomery, B. (Bruce); Seiler, R. (Roland); P.C. Black (Peter C.); J.L. Boormans (Joost); Dall′Era, M. (Marc); Davincioni, E. (Elai); Douglas, J. (James); Gibb, E.A. (Ewan A.); B.W. van Rhijn (Bas); M.S. van der Heijden (Michiel); Hsieh, A.C. (Andrew C.); Wright, J.L. (Jonathan L.); Lam, H.-M. (Hung-Ming)

2018-01-01

textabstractBackground: The mechanistic target of rapamycin (mTOR) has been implicated in driving tumor biology in multiple malignancies, including urothelial carcinoma (UC). We investigate how mTOR and phosphorylated mTOR (pmTOR) protein expression correlate with chemoresponsiveness in the tumor

Indian Ocean surface winds from NCMRWF analysis as compared

Indian Academy of Sciences (India)

The quality of the surface wind analysis at the National Centre for Medium Range Weather Forecasts (NCMRWF), New Delhi over the tropical Indian Ocean and its improvement in 2001 are examined by comparing it with in situ buoy measurements and satellite derived surface winds from NASA QuikSCAT satellite (QSCT) ...

Comparative analysis of methods for classification in predicting the quality of bread

OpenAIRE

E. A. Balashova; V. K. Bitjukov; E. A. Savvina

2013-01-01

The comparative analysis of classification methods of two-stage cluster and discriminant analysis and neural networks was performed. System of informative signs which classifies with a minimum of errors has been proposed.

Taxation and Gender Equity: A Comparative Analysis of Direct and ...

International Development Research Centre (IDRC) Digital Library (Canada)

2010-06-10

Jun 10, 2010 ... Taxation and Gender Equity: A Comparative Analysis of Direct and Indirect Taxes in Developing and Developed Countries ... This highly original book is essential reading for everyone concerned with equality in taxation.

Analogy of ISSR and RAPD markers for comparative analysis of ...

African Journals Online (AJOL)

Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. S Gupta, M Srivastava, GP Mishra, PK Naik, RS Chauhan, SK Tiwari, M Kumar, R Singh ...

Comparative analysis as a basic research orientation: Key methodological problems

Directory of Open Access Journals (Sweden)

N P Narbut

2015-12-01

Full Text Available To date, the Sociological Laboratory of the Peoples’ Friendship University of Russia has accumulated a vast experience in the field of cross-cultural studies reflected in the publications based on the results of mass surveys conducted in Moscow, Maikop, Beijing, Guangzhou, Prague, Belgrade, and Pristina. However, these publications mainly focus on the comparisons of the empirical data rather than methodological and technical issues, that is why the aim of this article is to identify key problems of the comparative analysis in cross-cultural studies that become evident only if you conduct an empirical research yourself - from the first step of setting the problem and approving it by all the sides (countries involved to the last step of interpreting and comparing the data obtained. The authors are sure that no sociologist would ever doubt the necessity and importance of comparative analysis in the broadest sense of the word, but at the same time very few are ready to discuss its key methodological challenges and prefer to ignore them completely. We summarize problems of the comparative analysis in sociology as follows: (1 applying research techniques to the sample in another country - both in translating and adapting them to different social realities and worldview (in particular, the problematic status of standardization and qualitative approach; (2 choosing “right” respondents to question and relevant cases (cultures to study; (3 designing the research scheme, i.e. justifying the sequence of steps (what should go first - methodology or techniques; (4 accepting the procedures that are correct within one country for cross-cultural work (whether or not that is an appropriate choice.

Institutional arrangements of Currency Boards - Comparative Macroeconomic Analysis

OpenAIRE

Lubomira Anastassova

1999-01-01

This paper is concentrated on the comparative macroeconomic analysis of the differences stemming from the extent to which the institutional framework of the currency board arrangement is implemented in the legal and regulatory systems in the different countries. The main objective of taking into consideration and examining the currency board institutional arrangements is to distinguish between the impact that currency board countries and countries with pegged exchange rate have on different m...

A comparative analysis of the perception and understanding of ...

African Journals Online (AJOL)

A comparative analysis of the perception and understanding of physical education and school sport among South African children aged 6-15 years. ... specifically with regard to 'feeling' about PE and SS, 'values' (importance) of PE and SS, 'comparison' of PE and SS with other school subjects and 'self-rating' on PE and SS.

In Vitro Efficacy and Mechanistic Role of Indocyanine Green as a Photodynamic Therapy Agent for Human Melanoma

Energy Technology Data Exchange (ETDEWEB)

Mamoon, A.; Gamal-Eldeen, A; Ruppel, M; Smith, R; Tsang, T; Miller, L

2009-01-01

Photodynamic therapy (PDT) is a promising treatment for superficial cancer. However, poor therapeutic results have been reported for melanoma, due to the high melanin content. Indocyanine green (ICG) has near infrared absorption (700-800nm) and melanins do not absorb strongly in this area. This study explores the efficiency of ICG as a PDT agent for human melanoma, and its mechanistic role in the cell death pathway.

Chirality-Controlled Growth of Single-Wall Carbon Nanotubes Using Vapor Phase Epitaxy: Mechanistic Understanding and Scalable Production

Science.gov (United States)

2016-09-15

AFRL-AFOSR-VA-TR-2016-0319 Chirality -Controlled Growth of Single-Wall Carbon Nanotubes Using Vapor Phase Epitaxy: Mechanistic Understanding and...TELEPHONE NUMBER (Include area code) DISTRIBUTION A: Distribution approved for public release. 15-06-2016 final Jun 2014 - Jun 2016 Chirality ...for Public Release; Distribution is Unlimited. In this report, we present our efforts in establishing a novel and effective approach for chirality

Comparative Analysis of Resonant Converters for Energy Storage Systems

Directory of Open Access Journals (Sweden)

Vuchev Stoyan

2017-01-01

Full Text Available The following paperwork presents a comparative analysis of multiphase resonant converters for applications in energy storage systems. Models of the examined converters are developed in the software environments of MATLAB and LTspice. Results from the simulation examination of the converters during charging of supercapacitors and rechargeable batteries are presented. These results are compared to results obtained from experimental examination of the converters via a laboratory stand. For the purposes of the experimental examination, a control system is developed on the base of a virtual instrument in LabVIEW. The advantages and disadvantages of the different converters are discussed.

Uncertainty analysis in comparative NAA applied to geological and biological matrices

International Nuclear Information System (INIS)

Zahn, Guilherme S.; Ticianelli, Regina B.; Lange, Camila N.; Favaro, Deborah I.T.; Figueiredo, Ana M.G.

2015-01-01

Comparative nuclear activation analysis is a multielemental primary analytical technique that may be used in a rather broad spectrum of matrices with minimal-to-none sample preprocessing. Although the total activation of a chemical element in a sample depends on a rather large set of parameters, when the sample is irradiated together with a well-known comparator, most of these parameters are crossed out and the concentration of that element can be determined simply by using the activities and masses of the comparator and the sample, the concentration of this chemical element in the sample, the half-life of the formed radionuclide and the time between counting the sample and the comparator. This simplification greatly reduces not only the calculations required, but also the uncertainty associated with the measurement; nevertheless, a cautious analysis must be carried out in order to make sure all relevant uncertainties are properly treated, so that the final result can be as representative of the measurement as possible. In this work, this analysis was performed for geological matrices, where concentrations of the interest nuclides are rather high, but so is the density and average atomic number of the sample, as well as for a biological matrix, in order to allow for a comparison. The results show that the largest part of the uncertainty comes from the activity measurements and from the concentration of the comparator, and that while the influence of time-related terms in the final uncertainty can be safely neglected, the uncertainty in the masses may be relevant under specific circumstances. (author)

Uncertainty analysis in comparative NAA applied to geological and biological matrices

Energy Technology Data Exchange (ETDEWEB)

Zahn, Guilherme S.; Ticianelli, Regina B.; Lange, Camila N.; Favaro, Deborah I.T.; Figueiredo, Ana M.G., E-mail: gzahn@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2015-07-01

Comparative nuclear activation analysis is a multielemental primary analytical technique that may be used in a rather broad spectrum of matrices with minimal-to-none sample preprocessing. Although the total activation of a chemical element in a sample depends on a rather large set of parameters, when the sample is irradiated together with a well-known comparator, most of these parameters are crossed out and the concentration of that element can be determined simply by using the activities and masses of the comparator and the sample, the concentration of this chemical element in the sample, the half-life of the formed radionuclide and the time between counting the sample and the comparator. This simplification greatly reduces not only the calculations required, but also the uncertainty associated with the measurement; nevertheless, a cautious analysis must be carried out in order to make sure all relevant uncertainties are properly treated, so that the final result can be as representative of the measurement as possible. In this work, this analysis was performed for geological matrices, where concentrations of the interest nuclides are rather high, but so is the density and average atomic number of the sample, as well as for a biological matrix, in order to allow for a comparison. The results show that the largest part of the uncertainty comes from the activity measurements and from the concentration of the comparator, and that while the influence of time-related terms in the final uncertainty can be safely neglected, the uncertainty in the masses may be relevant under specific circumstances. (author)

Four Mechanistic Models of Peer Influence on Adolescent Cannabis Use.

Science.gov (United States)

Caouette, Justin D; Feldstein Ewing, Sarah W

2017-06-01

Most adolescents begin exploring cannabis in peer contexts, but the neural mechanisms that underlie peer influence on adolescent cannabis use are still unknown. This theoretical overview elucidates the intersecting roles of neural function and peer factors in cannabis use in adolescents. Novel paradigms using functional magnetic resonance imaging (fMRI) in adolescents have identified distinct neural mechanisms of risk decision-making and incentive processing in peer contexts, centered on reward-motivation and affect regulatory neural networks; these findings inform a theoretical model of peer-driven cannabis use decisions in adolescents. We propose four "mechanistic profiles" of social facilitation of cannabis use in adolescents: (1) peer influence as the primary driver of use; (2) cannabis exploration as the primary driver, which may be enhanced in peer contexts; (3) social anxiety; and (4) negative peer experiences. Identification of "neural targets" involved in motivating cannabis use may inform clinicians about which treatment strategies work best in adolescents with cannabis use problems, and via which social and neurocognitive processes.

Mechanistic Approach to Understanding the Toxicity of the Azole Fungicide Triadimefon to a Nontarget Aquatic Insect and Implications for Exposure Assessment

Science.gov (United States)

We utilized mechanistic and stereoselective based in vitro metabolism assays and sublethal exposures of triadimefon to gain insight into the extent of carbonyl reduction and the toxic mode of action of triadimefon with black fly (Diptera: Simuliidae) larvae.

Statistics Education Research in Malaysia and the Philippines: A Comparative Analysis

Science.gov (United States)

Reston, Enriqueta; Krishnan, Saras; Idris, Noraini

2014-01-01

This paper presents a comparative analysis of statistics education research in Malaysia and the Philippines by modes of dissemination, research areas, and trends. An electronic search for published research papers in the area of statistics education from 2000-2012 yielded 20 for Malaysia and 19 for the Philippines. Analysis of these papers showed…

Comparative analysis of methods for classification in predicting the quality of bread

Directory of Open Access Journals (Sweden)

E. A. Balashova

2013-01-01

Full Text Available The comparative analysis of classification methods of two-stage cluster and discriminant analysis and neural networks was performed. System of informative signs which classifies with a minimum of errors has been proposed.

Mechanistic Perspectives of Maslinic Acid in Targeting Inflammation

Directory of Open Access Journals (Sweden)

Wei Hsum Yap

2015-01-01

Full Text Available Chronic inflammation drives the development of various pathological diseases such as rheumatoid arthritis, atherosclerosis, multiple sclerosis, and cancer. The arachidonic acid pathway represents one of the major mechanisms for inflammation. Prostaglandins (PGs are lipid products generated from arachidonic acid by the action of cyclooxygenase (COX enzymes and their activity is blocked by nonsteroidal anti-inflammatory drugs (NSAIDS. The use of natural compounds in regulation of COX activity/prostaglandins production is receiving increasing attention. In Mediterranean diet, olive oil and table olives contain significant dietary sources of maslinic acid. Maslinic acid is arising as a safe and novel natural pentacyclic triterpene which has protective effects against chronic inflammatory diseases in various in vivo and in vitro experimental models. Understanding the anti-inflammatory mechanism of maslinic acid is crucial for its development as a potential dietary nutraceutical. This review focuses on the mechanistic action of maslinic acid in regulating the inflammation pathways through modulation of the arachidonic acid metabolism including the nuclear factor-kappa B (NF-κB/COX-2 expression, upstream protein kinase signaling, and phospholipase A2 enzyme activity. Further investigations may provide insight into the mechanism of maslinic acid in regulating the molecular targets and their associated pathways in response to specific inflammatory stimuli.

Comparative analysis through probability distributions of a data set

Science.gov (United States)

Cristea, Gabriel; Constantinescu, Dan Mihai

2018-02-01

In practice, probability distributions are applied in such diverse fields as risk analysis, reliability engineering, chemical engineering, hydrology, image processing, physics, market research, business and economic research, customer support, medicine, sociology, demography etc. This article highlights important aspects of fitting probability distributions to data and applying the analysis results to make informed decisions. There are a number of statistical methods available which can help us to select the best fitting model. Some of the graphs display both input data and fitted distributions at the same time, as probability density and cumulative distribution. The goodness of fit tests can be used to determine whether a certain distribution is a good fit. The main used idea is to measure the "distance" between the data and the tested distribution, and compare that distance to some threshold values. Calculating the goodness of fit statistics also enables us to order the fitted distributions accordingly to how good they fit to data. This particular feature is very helpful for comparing the fitted models. The paper presents a comparison of most commonly used goodness of fit tests as: Kolmogorov-Smirnov, Anderson-Darling, and Chi-Squared. A large set of data is analyzed and conclusions are drawn by visualizing the data, comparing multiple fitted distributions and selecting the best model. These graphs should be viewed as an addition to the goodness of fit tests.

Blood-brain barrier disruption: mechanistic links between Western diet consumption and dementia

Directory of Open Access Journals (Sweden)

Ted Menghsiung Hsu

2014-05-01

Full Text Available Both obesity and Alzheimer’s disease are major health burdens in Western societies. While commonly viewed as having separate etiologies, this review highlights data suggesting that intake of Western diets, diets high in saturated fatty acids and simple carbohydrates, may pose a common environmental risk factor contributing to the development of both of these adverse pathologies. We discuss the effects of Western Diet intake on learning and memory processes that are dependent on the hippocampus, as well as the importance of this brain region in both obesity development and the onset of Alzheimer’s and other dementias. A putative mechanism is discussed that mechanistically links Western diet consumption, blood brain barrier degradation, and subsequent hippocampal damage and dementia pathology.

Insight into the hydraulics and resilience of Ponderosa pine seedlings using a mechanistic ecohydrologic model

Science.gov (United States)

Maneta, M. P.; Simeone, C.; Dobrowski, S.; Holden, Z.; Sapes, G.; Sala, A.; Begueria, S.

2017-12-01

In semiarid regions, drought-induced seedling mortality is considered to be caused by failure in the tree hydraulic column. Understanding the mechanisms that cause hydraulic failure and death in seedlings is important, among other things, to diagnose where some tree species may fail to regenerate, triggering demographic imbalances in the forest that could result in climate-driven shifts of tree species. Ponderosa pine is a common lower tree line species in the western US. Seedlings of ponderosa pine are often subject to low soil water potentials, which require lower water potentials in the xylem and leaves to maintain the negative pressure gradient that drives water upward. The resilience of the hydraulic column to hydraulic tension is species dependent, but from greenhouse experiments, we have identified general tension thresholds beyond which loss of xylem conductivity becomes critical, and mortality in Ponderosa pine seedlings start to occur. We describe this hydraulic behavior of plants using a mechanistic soil-vegetation-atmosphere transfer model. Before we use this models to understand water-stress induced seedling mortality at the landscape scale, we perform a modeling analysis of the dynamics of soil moisture, transpiration, leaf water potential and loss of plant water conductivity using detailed data from our green house experiments. The analysis is done using a spatially distributed model that simulates water fluxes, energy exchanges and water potentials in the soil-vegetation-atmosphere continuum. Plant hydraulic and physiological parameters of this model were calibrated using Monte Carlo methods against information on soil moisture, soil hydraulic potential, transpiration, leaf water potential and percent loss of conductivity in the xylem. This analysis permits us to construct a full portrait of the parameter space for Ponderosa pine seedling and generate posterior predictive distributions of tree response to understand the sensitivity of transpiration

Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Metal Fuel Radionuclide Release

International Nuclear Information System (INIS)

Grabaskas, David; Bucknor, Matthew; Jerden, James

2016-01-01

The development of an accurate and defensible mechanistic source term will be vital for the future licensing efforts of metal fuel, pool-type sodium fast reactors. To assist in the creation of a comprehensive mechanistic source term, the current effort sought to estimate the release fraction of radionuclides from metal fuel pins to the primary sodium coolant during fuel pin failures at a variety of temperature conditions. These release estimates were based on the findings of an extensive literature search, which reviewed past experimentation and reactor fuel damage accidents. Data sources for each radionuclide of interest were reviewed to establish release fractions, along with possible release dependencies, and the corresponding uncertainty levels. Although the current knowledge base is substantial, and radionuclide release fractions were established for the elements deemed important for the determination of offsite consequences following a reactor accident, gaps were found pertaining to several radionuclides. First, there is uncertainty regarding the transport behavior of several radionuclides (iodine, barium, strontium, tellurium, and europium) during metal fuel irradiation to high burnup levels. The migration of these radionuclides within the fuel matrix and bond sodium region can greatly affect their release during pin failure incidents. Post-irradiation examination of existing high burnup metal fuel can likely resolve this knowledge gap. Second, data regarding the radionuclide release from molten high burnup metal fuel in sodium is sparse, which makes the assessment of radionuclide release from fuel melting accidents at high fuel burnup levels difficult. This gap could be addressed through fuel melting experimentation with samples from the existing high burnup metal fuel inventory.

Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Metal Fuel Radionuclide Release

Energy Technology Data Exchange (ETDEWEB)

Grabaskas, David [Argonne National Lab. (ANL), Argonne, IL (United States); Bucknor, Matthew [Argonne National Lab. (ANL), Argonne, IL (United States); Jerden, James [Argonne National Lab. (ANL), Argonne, IL (United States)

2016-02-01

The development of an accurate and defensible mechanistic source term will be vital for the future licensing efforts of metal fuel, pool-type sodium fast reactors. To assist in the creation of a comprehensive mechanistic source term, the current effort sought to estimate the release fraction of radionuclides from metal fuel pins to the primary sodium coolant during fuel pin failures at a variety of temperature conditions. These release estimates were based on the findings of an extensive literature search, which reviewed past experimentation and reactor fuel damage accidents. Data sources for each radionuclide of interest were reviewed to establish release fractions, along with possible release dependencies, and the corresponding uncertainty levels. Although the current knowledge base is substantial, and radionuclide release fractions were established for the elements deemed important for the determination of offsite consequences following a reactor accident, gaps were found pertaining to several radionuclides. First, there is uncertainty regarding the transport behavior of several radionuclides (iodine, barium, strontium, tellurium, and europium) during metal fuel irradiation to high burnup levels. The migration of these radionuclides within the fuel matrix and bond sodium region can greatly affect their release during pin failure incidents. Post-irradiation examination of existing high burnup metal fuel can likely resolve this knowledge gap. Second, data regarding the radionuclide release from molten high burnup metal fuel in sodium is sparse, which makes the assessment of radionuclide release from fuel melting accidents at high fuel burnup levels difficult. This gap could be addressed through fuel melting experimentation with samples from the existing high burnup metal fuel inventory.

REM sleep behaviour disorder: prodromal and mechanistic insights for Parkinson's disease.

Science.gov (United States)

Tekriwal, Anand; Kern, Drew S; Tsai, Jean; Ince, Nuri F; Wu, Jianping; Thompson, John A; Abosch, Aviva

2017-05-01

Rapid eye movement (REM) sleep behaviour disorder (RBD) is characterised by complex motor enactment of dreams and is a potential prodromal marker of Parkinson's disease (PD). Of note, patients with PD observed during RBD episodes exhibit improved motor function, relative to baseline states during wake periods. Here, we review recent epidemiological and mechanistic findings supporting the prodromal value of RBD for PD, incorporating clinical and electrophysiological studies. Explanations for the improved motor function during RBD episodes are evaluated in light of recent publications. In addition, we present preliminary findings describing changes in the activity of the basal ganglia across the sleep-wake cycle that contribute to our understanding of RBD. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Comparative chemoreactome analysis of dexketoprofen, ketoprofen, and diclofenac

Directory of Open Access Journals (Sweden)

I. Yu. Torshin

2018-01-01

Full Text Available Cyclooxygenase-2 (COX-2 is the main targeted protein of non-steroidal anti-inflammatory drugs (NSAID; nevertheless, the latter substantially differ in pharmacological properties.Objective: to establish the spectrum of pharmacological actions of dexketoprofen, ketoprofen, and diclofenac, by using a chemoreactome analysis.Material and methods. A chemoinformation analysis was used to determine a list of the chemical structures closest to dexketoprofen. For each molecule, the investigators extracted the results of experimental measurements of the rheological properties of this molecule from databases and a chemoreactome analysis was carried out. The comparative chemoreactome analysis of the molecule of dexketoprofen and control molecules (ketoprofen, diclofenac could assess the biological activity of the studied molecule.Results and discussion. Unlike the molecules of comparison, dexketoprofen was found to be able to accumulate mainly in muscles, adipose tissue, and adrenal glands. The anti-inflammatory and analgesic effect of dexketoprofen can be carried out via modulation not only of the metabolism of prostaglandins, but also that of leukotrienes and encephalins, as well as via inhibition of metalloproteinases and glutamate receptors. In addition, the analysis showed a considerable difference in the interaction profiles of dexketoprofen, ketoprofen, and diclofenac with cytochrome P450 enzymes. Dexketoprofen can enhance the efficacy of anti-arrhythmic and antiadrenergic agents, whereas ketoprofen and diclofenac are able to negatively affect the metabolism of omega-3 polyunsaturated fatty acids and vitamin D.Conclusion. The chemoreactome analysis could identify the promising vasodilatory, antiplatelet, antidiabetic, and antitumor effects of dexketoprofen in addition to its main action. 

Simulating polar bear energetics during a seasonal fast using a mechanistic model.

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Paul D Mathewson

Full Text Available In this study we tested the ability of a mechanistic model (Niche Mapper™ to accurately model adult, non-denning polar bear (Ursus maritimus energetics while fasting during the ice-free season in the western Hudson Bay. The model uses a steady state heat balance approach, which calculates the metabolic rate that will allow an animal to maintain its core temperature in its particular microclimate conditions. Predicted weight loss for a 120 day fast typical of the 1990s was comparable to empirical studies of the population, and the model was able to reach a heat balance at the target metabolic rate for the entire fast, supporting use of the model to explore the impacts of climate change on polar bears. Niche Mapper predicted that all but the poorest condition bears would survive a 120 day fast under current climate conditions. When the fast extended to 180 days, Niche Mapper predicted mortality of up to 18% for males. Our results illustrate how environmental conditions, variation in animal properties, and thermoregulation processes may impact survival during extended fasts because polar bears were predicted to require additional energetic expenditure for thermoregulation during a 180 day fast. A uniform 3°C temperature increase reduced male mortality during a 180 day fast from 18% to 15%. Niche Mapper explicitly links an animal's energetics to environmental conditions and thus can be a valuable tool to help inform predictions of climate-related population changes. Since Niche Mapper is a generic model, it can make energetic predictions for other species threatened by climate change.

Simulating polar bear energetics during a seasonal fast using a mechanistic model.

Science.gov (United States)

Mathewson, Paul D; Porter, Warren P

2013-01-01

In this study we tested the ability of a mechanistic model (Niche Mapper™) to accurately model adult, non-denning polar bear (Ursus maritimus) energetics while fasting during the ice-free season in the western Hudson Bay. The model uses a steady state heat balance approach, which calculates the metabolic rate that will allow an animal to maintain its core temperature in its particular microclimate conditions. Predicted weight loss for a 120 day fast typical of the 1990s was comparable to empirical studies of the population, and the model was able to reach a heat balance at the target metabolic rate for the entire fast, supporting use of the model to explore the impacts of climate change on polar bears. Niche Mapper predicted that all but the poorest condition bears would survive a 120 day fast under current climate conditions. When the fast extended to 180 days, Niche Mapper predicted mortality of up to 18% for males. Our results illustrate how environmental conditions, variation in animal properties, and thermoregulation processes may impact survival during extended fasts because polar bears were predicted to require additional energetic expenditure for thermoregulation during a 180 day fast. A uniform 3°C temperature increase reduced male mortality during a 180 day fast from 18% to 15%. Niche Mapper explicitly links an animal's energetics to environmental conditions and thus can be a valuable tool to help inform predictions of climate-related population changes. Since Niche Mapper is a generic model, it can make energetic predictions for other species threatened by climate change.

A Comparative Analysis of Quadratics Unit in Singaporean, Turkish and IBDP Mathematics Textbooks

Directory of Open Access Journals (Sweden)

Reyhan Sağlam

2012-12-01

Full Text Available The purpose of this study was to analyze and compare the contents of the chapters on quadratics in three mathematics textbooks selected from Turkey, Singapore, and the International Baccalaureate Diploma Program (IBDP through content analysis. The analysis of mathematical content showed that the three textbooks have different approaches and priorities in terms of the positions of chapters and weights of the quadratics units, and the time allocated to them within the respective curricular programs. It was also found that the Turkish textbook covers a greater number of learning outcomes targeted for quadratics among the three mathematics syllabi, showing a detailed treatment of the topic compared to the other two textbooks.Key Words: Content analysis, international comparative studies, mathematics textbooks

Construction QA/QC systems: comparative analysis

International Nuclear Information System (INIS)

Willenbrock, J.H.; Shepard, S.

1980-01-01

An analysis which compares the quality assurance/quality control (QA/QC) systems adopted in the highway, nuclear power plant, and U.S. Navy construction areas with the traditional quality control approach used in building construction is presented. Full participation and support by the owner as well as the contractor and AE firm are required if a QA/QC system is to succeed. Process quality control, acceptance testing and quality assurance responsibilities must be clearly defined in the contract documents. The owner must audit these responsibilities. A contractor quality control plan, indicating the tasks which will be performed and the fact that QA/QC personnel are independent of project time/cost pressures should be submitted for approval. The architect must develop realistic specifications which consider the natural variability of material. Acceptance criteria based on the random sampling technique should be used. 27 refs

Comparative Genome Analysis of Basidiomycete Fungi

Energy Technology Data Exchange (ETDEWEB)

Riley, Robert; Salamov, Asaf; Morin, Emmanuelle; Nagy, Laszlo; Manning, Gerard; Baker, Scott; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Hibbett, David; Martin, Francis; Grigoriev, Igor

2012-03-19

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

Development of a mechanistically based computer simulation of nitrogen oxide absorption in packed towers

International Nuclear Information System (INIS)

Counce, R.M.

1981-01-01

A computer simulation for nitrogen oxide (NO/sub x/) scrubbing in packed towers was developed for use in process design and process control. This simulation implements a mechanistically based mathematical model, which was formulated from (1) an exhaustive literature review; (2) previous NO/sub x/ scrubbing experience with sieve-plate towers; and (3) comparisons of sequential sets of experiments. Nitrogen oxide scrubbing is characterized by simultaneous absorption and desorption phenomena: the model development is based on experiments designed to feature these two phenomena. The model was then successfully tested in experiments designed to put it in jeopardy

Mechanistic considerations used in the development of the probability of failure in transient increases in power (PROFIT) pellet-zircaloy cladding (thermo-mechanical-chemical) interactions (pci) fuel failure model

International Nuclear Information System (INIS)

Pankaskie, P.J.

1980-05-01

A fuel Pellet-Zircaloy Cladding (thermo-mechanical-chemical) interactions (PCI) failure model for estimating the Probability of Failure in Transient Increases in Power (PROFIT) was developed. PROFIT is based on (1) standard statistical methods applied to available PCI fuel failure data and (2) a mechanistic analysis of the environmental and strain-rate-dependent stress versus strain characteristics of Zircaloy cladding. The statistical analysis of fuel failures attributable to PCI suggested that parameters in addition to power, transient increase in power, and burnup are needed to define PCI fuel failures in terms of probability estimates with known confidence limits. The PROFIT model, therefore, introduces an environmental and strain-rate dependent Strain Energy Absorption to Failure (SEAF) concept to account for the stress versus strain anomalies attributable to interstitial-dislocation interaction effects in the Zircaloy cladding

Comparative analysis of proliferation resistance assessment methodologies

International Nuclear Information System (INIS)

Takaki, Naoyuki; Kikuchi, Masahiro; Inoue, Naoko; Osabe, Takeshi

2005-01-01

Comparative analysis of the methodologies was performed based on the discussions in the international workshop on 'Assessment Methodology of Proliferation Resistance for Future Nuclear Energy Systems' held in Tokyo, on March 2005. Through the workshop and succeeding considerations, it is clarified that the proliferation resistance assessment methodologies are affected by the broader nuclear options being pursued and also by the political situations of the state. Even the definition of proliferation resistance, despite the commonality of fundamental issues, derives from perceived threat and implementation circumstances inherent to the larger programs. Deep recognitions of the 'difference' among communities would help us to make further essential and progressed discussion with harmonization. (author)

2004/2008 labour market information comparative analysis report

International Nuclear Information System (INIS)

2009-01-01

The electricity sector has entered into a phase of both challenges and opportunities. Challenges include workforce retirement, labour shortages, and increased competition from other employers to attract and retain the skilled people required to deliver on the increasing demand for electricity in Canada. The electricity sector in Canada is also moving into a new phase, whereby much of the existing infrastructure is either due for significant upgrades, or complete replacement. The increasing demand for electricity means that increased investment and capital expenditure will need to be put toward building new infrastructure altogether. The opportunities for the electricity industry will lie in its ability to effectively and efficiently react to these challenges. The purpose of this report was to provide employers and stakeholders in the sector with relevant and current trend data to help them make appropriate policy and human resource decisions. The report presented a comparative analysis of a 2004 Canadian Electricity Association employer survey with a 2008 Electricity Sector Council employer survey. The comparative analysis highlighted trends and changes that emerged between the 2004 and 2008 studies. Specific topics that were addressed included overall employment trends; employment diversity in the sector; age of non-support staff; recruitment; and retirements and pension eligibility. Recommendations were also offered. It was concluded that the electricity sector could benefit greatly from implementing on-going recruitment campaigns. refs., tabs., figs

Comparative study of approaches to estimate pipe break frequencies

Energy Technology Data Exchange (ETDEWEB)

Simola, K.; Pulkkinen, U.; Talja, H.; Saarenheimo, A.; Karjalainen-Roikonen, P. [VTT Industrial Systems (Finland)

2002-12-01

The report describes the comparative study of two approaches to estimate pipe leak and rupture frequencies for piping. One method is based on a probabilistic fracture mechanistic (PFM) model while the other one is based on statistical estimation of rupture frequencies from a large database. In order to be able to compare the approaches and their results, the rupture frequencies of some selected welds have been estimated using both of these methods. This paper highlights the differences both in methods, input data, need and use of plant specific information and need of expert judgement. The study focuses on one specific degradation mechanism, namely the intergranular stress corrosion cracking (IGSCC). This is the major degradation mechanism in old stainless steel piping in BWR environment, and its growth is influenced by material properties, stresses and water chemistry. (au)

Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non-targeted analysis of comparative samples.

Science.gov (United States)

Titaley, Ivan A; Ogba, O Maduka; Chibwe, Leah; Hoh, Eunha; Cheong, Paul H-Y; Simonich, Staci L Massey

2018-03-16

Non-targeted analysis of environmental samples, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO ® ChromaTOF ® software and facilitates selection of analytes of interest based on peak area comparison between comparative samples. We used data from polycyclic aromatic hydrocarbon (PAH) contaminated soil, pre- and post-bioremediation, to assess the effectiveness of OCTpy in facilitating the selection of analytes that have formed or degraded following treatment. Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature. Based on this list, 63-100% of the candidate analytes identified by a highly trained individual were also selected by OCTpy. This process was accomplished in several minutes per sample, whereas manual data analysis took several hours per sample. OCTpy automates the analysis of complex mixtures of comparative samples, reduces the potential for human error during heavy data handling and decreases data analysis time by at least tenfold. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparing robotic, laparoscopic and open cystectomy: a systematic review and meta-analysis

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Thomas Fonseka

2015-03-01

Full Text Available Objective: To conduct a systematic review and meta-analysis comparing outcomes between Open Radical Cystectomy (ORC, Laparoscopic Radical Cystectomy (LRC and Robot-assisted Radical Cystectomy (RARC. RARC is to be compared to LRC and ORC and LRC compared to ORC. Material and methods: A systematic review of the literature was conducted, collating studies comparing RARC, LRC and ORC. Surgical and oncological outcome data were extracted and a meta-analysis was performed. Results: Twenty-four studies were selected with total of 2,104 cases analyzed. RARC had a longer operative time (OPT compared to LRC with no statistical difference between length of stay (LOS and estimated blood loss (EBL. RARC had a significantly shorter LOS, reduced EBL, lower complication rate and longer OPT compared to ORC. There were no significant differences regarding lymph node yield (LNY and positive surgical margins (PSM. LRC had a reduced EBL, shorter LOS and increased OPT compared to ORC. There was no significant difference regarding LNY. Conclusion: RARC is comparable to LRC with better surgical results than ORC. LRC has better surgical outcomes than ORC. With the unique technological features of the robotic surgical system and increasing trend of intra-corporeal reconstruction it is likely that RARC will become the surgical option of choice.

A dynamic, mechanistic model of metabolism in adipose tissue of lactating dairy cattle.

Science.gov (United States)

McNamara, J P; Huber, K; Kenéz, A

2016-07-01

Research in dairy cattle biology has resulted in a large body of knowledge on nutrition and metabolism in support of milk production and efficiency. This quantitative knowledge has been compiled in several model systems to balance and evaluate rations and predict requirements. There are also systems models for metabolism and reproduction in the cow that can be used to support research programs. Adipose tissue plays a significant role in the success and efficiency of lactation, and recent research has resulted in several data sets on genomic differences and changes in gene transcription of adipose tissue in dairy cattle. To fully use this knowledge, we need to build and expand mechanistic, dynamic models that integrate control of metabolism and production. Therefore, we constructed a second-generation dynamic, mechanistic model of adipose tissue metabolism of dairy cattle. The model describes the biochemical interconversions of glucose, acetate, β-hydroxybutyrate (BHB), glycerol, C16 fatty acids, and triacylglycerols. Data gathered from our own research and published references were used to set equation forms and parameter values. Acetate, glucose, BHB, and fatty acids are taken up from blood. The fatty acids are activated to the acyl coenzyme A moieties. Enzymatically catalyzed reactions are explicitly described with parameters including maximal velocity and substrate sensitivity. The control of enzyme activity is partially carried out by insulin and norepinephrine, portraying control in the cow. Model behavior was adequate, with sensitive responses to changing substrates and hormones. Increased nutrient uptake and increased insulin stimulate triacylglycerol synthesis, whereas a reduction in nutrient availability or increase in norepinephrine increases triacylglycerol hydrolysis and free fatty acid release to blood. This model can form a basis for more sophisticated integration of existing knowledge and future studies on metabolic efficiency of dairy cattle

Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects

Energy Technology Data Exchange (ETDEWEB)

Shrestha, Ruben [Department; Huang, Gaochao [Department; Meekins, David A. [Department; Geisbrecht, Brian V. [Department; Li, Ping [Department

2017-08-18

Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases that have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been determined for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand and two channels at diameters of ~3.0 and 8.0 Å lead to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs’ bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pD 3.5 suggested that compound 0 deprotonation by the distal aspartate is rate-limiting in the formation of compound I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with compound I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in ElDyP is mechanistically important and may explain the enzyme’s adoption of two-electron reduction for compound I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining ElDyP’s optimum acidic pH. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs’ lignolytic activity.

Activation of phosphoinositide 3-kinase/Akt/mechanistic target of rapamycin pathway and response to everolimus in endocrine receptor-positive metastatic breast cancer – A retrospective pilot analysis and viewpoint

Directory of Open Access Journals (Sweden)

Jyoti Bajpai

2017-01-01

Full Text Available Introduction: Biomarkers predictive of response to mechanistic target of rapamycin (mTOR inhibitor, everolimus, in endocrine receptor (ER-positive metastatic breast cancer (MBC are a work in progress. We evaluated the feasibility of directly measuring mTOR activity and phosphatase and tensin homolog (PTEN expression and correlating their expression with response and survival. Materials and Methods: MBC patients who received everolimus with endocrine therapy (ET after progression on an aromatase inhibitor and had adequate tissue preservation for estimation of mTOR activity and PTEN expression were selected for analysis from a prospectively maintained database. Progression-free survival (PFS and overall survival (OS were estimated by Kaplan–Meier method, and correlation between mTOR activity and PTEN expression with survival was done by log-rank test. Results: Thirteen ER-positive MBC patients were available for analysis. PTEN expression was lost in 11/13 (84.6% patients and retained in 2/13 patients (15.4%. mTOR activity was absent in four patients (30.7%, weak in six patients (46.1%, and moderate in 3 patients (23.2%. Median PFS for the entire population was 2.5 months while median OS was not reached. Patients with an absent mTOR activity showed a longer PFS (5 vs. 1.5 vs. 2 months than those with weak and moderate activity, respectively (P = 0.043. There was no correlation between loss of PTEN expression and PFS. Conclusions: Measurement of direct mTOR activity in patients with MBC receiving everolimus/ET combination appears feasible. Absent mTOR activity may predict for longer PFS with everolimus-ET combination and requires further study.

Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii genome.

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Byrappa Venkatesh

2007-04-01

Full Text Available Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.

Mechanistic modeling for mammography screening risks

International Nuclear Information System (INIS)

Bijwaard, Harmen

2008-01-01

Full text: Western populations show a very high incidence of breast cancer and in many countries mammography screening programs have been set up for the early detection of these cancers. Through these programs large numbers of women (in the Netherlands, 700.000 per year) are exposed to low but not insignificant X-ray doses. ICRP based risk estimates indicate that the number of breast cancer casualties due to mammography screening can be as high as 50 in the Netherlands per year. The number of lives saved is estimated to be much higher, but for an accurate calculation of the benefits of screening a better estimate of these risks is indispensable. Here it is attempted to better quantify the radiological risks of mammography screening through the application of a biologically based model for breast tumor induction by X-rays. The model is applied to data obtained from the National Institutes of Health in the U.S. These concern epidemiological data of female TB patients who received high X-ray breast doses in the period 1930-1950 through frequent fluoroscopy of their lungs. The mechanistic model that is used to describe the increased breast cancer incidence is based on an earlier study by Moolgavkar et al. (1980), in which the natural background incidence of breast cancer was modeled. The model allows for a more sophisticated extrapolation of risks to the low dose X-ray exposures that are common in mammography screening and to the higher ages that are usually involved. Furthermore, it allows for risk transfer to other (non-western) populations. The results have implications for decisions on the frequency of screening, the number of mammograms taken at each screening, minimum and maximum ages for screening and the transfer to digital equipment. (author)

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

Science.gov (United States)

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

2018-03-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

Science.gov (United States)

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E.

2018-01-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns. PMID:29657753

Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

Science.gov (United States)

Robins, Lori I; Fogle, Emily J; Marlier, John F

2015-11-01

The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluating the mechanistic evidence and key data gaps in assessing the potential carcinogenicity of carbon nanotubes and nanofibers in humans

NARCIS (Netherlands)

Kuempel, Eileen D; Jaurand, Marie-Claude; Møller, Peter; Morimoto, Yasuo; Kobayashi, Norihiro; Pinkerton, Kent E; Sargent, Linda M; Vermeulen, Roel C H; Fubini, Bice; Kane, Agnes B

2017-01-01

In an evaluation of carbon nanotubes (CNTs) for the IARC Monograph 111, the Mechanisms Subgroup was tasked with assessing the strength of evidence on the potential carcinogenicity of CNTs in humans. The mechanistic evidence was considered to be not strong enough to alter the evaluations based on the

Skull Development, Ossification Pattern, and Adult Shape in the Emerging Lizard Model Organism Pogona vitticeps: A Comparative Analysis With Other Squamates

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Joni Ollonen

2018-03-01

Full Text Available The rise of the Evo-Devo field and the development of multidisciplinary research tools at various levels of biological organization have led to a growing interest in researching for new non-model organisms. Squamates (lizards and snakes are particularly important for understanding fundamental questions about the evolution of vertebrates because of their high diversity and evolutionary innovations and adaptations that portrait a striking body plan change that reached its extreme in snakes. Yet, little is known about the intricate connection between phenotype and genotype in squamates, partly due to limited developmental knowledge and incomplete characterization of embryonic development. Surprisingly, squamate models have received limited attention in comparative developmental studies, and only a few species examined so far can be considered as representative and appropriate model organism for mechanistic Evo-Devo studies. Fortunately, the agamid lizard Pogona vitticeps (central bearded dragon is one of the most popular, domesticated reptile species with both a well-established history in captivity and key advantages for research, thus forming an ideal laboratory model system and justifying his recent use in reptile biology research. We first report here the complete post-oviposition embryonic development for P. vitticeps based on standardized staging systems and external morphological characters previously defined for squamates. Whereas the overall morphological development follows the general trends observed in other squamates, our comparisons indicate major differences in the developmental sequence of several tissues, including early craniofacial characters. Detailed analysis of both embryonic skull development and adult skull shape, using a comparative approach integrating CT-scans and gene expression studies in P. vitticeps as well as comparative embryology and 3D geometric morphometrics in a large dataset of lizards and snakes, highlights

Modeling of the pyruvate production with Escherichia coli: comparison of mechanistic and neural networks-based models.

Science.gov (United States)

Zelić, B; Bolf, N; Vasić-Racki, D

2006-06-01

Three different models: the unstructured mechanistic black-box model, the input-output neural network-based model and the externally recurrent neural network model were used to describe the pyruvate production process from glucose and acetate using the genetically modified Escherichia coli YYC202 ldhA::Kan strain. The experimental data were used from the recently described batch and fed-batch experiments [ Zelić B, Study of the process development for Escherichia coli-based pyruvate production. PhD Thesis, University of Zagreb, Faculty of Chemical Engineering and Technology, Zagreb, Croatia, July 2003. (In English); Zelić et al. Bioproc Biosyst Eng 26:249-258 (2004); Zelić et al. Eng Life Sci 3:299-305 (2003); Zelić et al Biotechnol Bioeng 85:638-646 (2004)]. The neural networks were built out of the experimental data obtained in the fed-batch pyruvate production experiments with the constant glucose feed rate. The model validation was performed using the experimental results obtained from the batch and fed-batch pyruvate production experiments with the constant acetate feed rate. Dynamics of the substrate and product concentration changes was estimated using two neural network-based models for biomass and pyruvate. It was shown that neural networks could be used for the modeling of complex microbial fermentation processes, even in conditions in which mechanistic unstructured models cannot be applied.

ANALYSIS OF ENTREPRENEURSHIP IN ROMANIA COMPARATIVE WITH THE EU COUNTRIES -27

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Tudor Pendiuc

2013-12-01

Full Text Available Entrepreneurship is a socio-economic phenomenon of great complexity, defining the market economy system. As the business environment becomes more complex and competitive, the entrepreneurs must become more creative and receptive to what is new and innovative. For Romania the promotion and development of entrepreneurship were a central objective in the last decade for job creation, competitiveness growth and sustainable economic development. Regardless of the method chosen to develop a business, the entrepreneur must operate with criteria of rationality in terms of choices, decisions and performance evaluation. This work aims a comparative analysis of the main issues concerning the development of entrepreneurship in Romania compared to other EU countries. It emphasizes the following aspects: a option on the status of employee/contractor; b the important factors in the decision on starting/taking over a business; c difficulties to start/taking over a business. Based on the analysis were resulted conclusions on the main economic and social features of entrepreneurship in Romania compared to other European Union member states. It was stressed the importance of entrepreneurship development on the Romanian economy, by analyzing the factors that encourage or discourage the entrepreneurship. The research was conducted using a variety of bibliographic sources such as statistics, analysis, reports, professional articles.

Comparative secretome analysis of rat stomach under different nutritional status

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Lucia L. Senin

2015-06-01

Full Text Available The fact that gastric surgery is at the moment the most effective treatment to fight against obesity highlights the relevance of gastric derived proteins as potential targets to treat this pathology. Taking advantage of a previously established gastric explant model for endocrine studies, the proteomic analysis of gastric secretome was performed. To validate this gastric explant system for proteomic analysis, the identification of ghrelin, a classical gastric derived peptide, was performed by MS. In addition, the differential analysis of gastric secretomes under differential nutritional status (control feeding vs fasting vs re-feeding was performed. The MS identified proteins are showed in the present manuscript. The data supplied in this article is related to the research article entitled “Comparative secretome analysis of rat stomach under different nutritional status” [1].

Groundwater arsenic removal by coagulation using ferric(III) sulfate and polyferric sulfate: A comparative and mechanistic study.

Science.gov (United States)

Cui, Jinli; Jing, Chuanyong; Che, Dongsheng; Zhang, Jianfeng; Duan, Shuxuan

2015-06-01

Elevated arsenic (As) in groundwater poses a great threat to human health. Coagulation using mono- and poly-Fe salts is becoming one of the most cost-effective processes for groundwater As removal. However, a limitation comes from insufficient understanding of the As removal mechanism from groundwater matrices in the coagulation process, which is critical for groundwater treatment and residual solid disposal. Here, we overcame this hurdle by utilizing microscopic techniques to explore molecular As surface complexes on the freshly formed Fe flocs and compared ferric(III) sulfate (FS) and polyferric sulfate (PFS) performance, and finally provided a practical solution in As-geogenic areas. FS and PFS exhibited a similar As removal efficiency in coagulation and coagulation/filtration in a two-bucket system using 5mg/L Ca(ClO)2. By using the two-bucket system combining coagulation and sand filtration, 500 L of As-safe water (<10 μg/L) was achieved during five treatment cycles by washing the sand layer after each cycle. Fe k-edge X-ray absorption near-edge structure (XANES) and As k-edge extended X-ray absorption fine structure (EXAFS) analysis of the solid residue indicated that As formed a bidentate binuclear complex on ferrihydrite, with no observation of scorodite or poorly-crystalline ferric arsenate. Such a stable surface complex is beneficial for As immobilization in the solid residue, as confirmed by the achievement of much lower leachate As (0.9 μg/L-0.487 mg/L) than the US EPA regulatory limit (5 mg/L). Finally, PFS is superior to FS because of its lower dose, much lower solid residue, and lower cost for As-safe drinking water. Copyright © 2015. Published by Elsevier B.V.

CONPAS 1.0 (CONtainment Performance Analysis System). User's manual

International Nuclear Information System (INIS)

Ahn, Kwang Il; Jin, Young Ho

1996-04-01

CONPAS (CONtainment Performance Analysis System) is a verified computer code package to integrate the numerical, graphical, and results-operation aspects of Level 2 probabilistic safety assessments (PSA) for nuclear power plants automatically under a PC window environment. Compared with the existing DOS-based computer codes for Level 2 PSA, the most important merit of the window-based computer code is that user can easily describe and quantify the accident progression models, and manipulate the resultant outputs in a variety of ways. As a main logic for accident progression analysis, CONPAS employs a concept of the small containment phenomenological event tree (CPET) helpful to trace out visually individual accident progressions and of the large supporting event tree (LSET) for its detailed quantification. For the integrated analysis of Level 2 PSA, the code utilizes four distinct, but closely related modules; (1) ET Editor for construction of several event tree models describing the accident progressions, (2) Computer for quantification of the constructed event trees and graphical display of the resultant outputs, (3) Text Editor for preparation of input decks for quanification and utilization of calculational results, and (4) Mechanistic Code Plotter for utilization of results obtained from severe accident analysis codes. Compared with other existing computer codes for Level 2 PSA, the CONPAS code provides several advanced features: computational aspects including systematic uncertainty analysis, importance analysis, sensitivity analysis and data interpretation, reporting aspects including tabling and graphic as well as user-friend interface. 10 refs. (Author) .new

Neo-Deterministic and Probabilistic Seismic Hazard Assessments: a Comparative Analysis

Science.gov (United States)

Peresan, Antonella; Magrin, Andrea; Nekrasova, Anastasia; Kossobokov, Vladimir; Panza, Giuliano F.

2016-04-01

Objective testing is the key issue towards any reliable seismic hazard assessment (SHA). Different earthquake hazard maps must demonstrate their capability in anticipating ground shaking from future strong earthquakes before an appropriate use for different purposes - such as engineering design, insurance, and emergency management. Quantitative assessment of maps performances is an essential step also in scientific process of their revision and possible improvement. Cross-checking of probabilistic models with available observations and independent physics based models is recognized as major validation procedure. The existing maps from the classical probabilistic seismic hazard analysis (PSHA), as well as those from the neo-deterministic analysis (NDSHA), which have been already developed for several regions worldwide (including Italy, India and North Africa), are considered to exemplify the possibilities of the cross-comparative analysis in spotting out limits and advantages of different methods. Where the data permit, a comparative analysis versus the documented seismic activity observed in reality is carried out, showing how available observations about past earthquakes can contribute to assess performances of the different methods. Neo-deterministic refers to a scenario-based approach, which allows for consideration of a wide range of possible earthquake sources as the starting point for scenarios constructed via full waveforms modeling. The method does not make use of empirical attenuation models (i.e. Ground Motion Prediction Equations, GMPE) and naturally supplies realistic time series of ground shaking (i.e. complete synthetic seismograms), readily applicable to complete engineering analysis and other mitigation actions. The standard NDSHA maps provide reliable envelope estimates of maximum seismic ground motion from a wide set of possible scenario earthquakes, including the largest deterministically or historically defined credible earthquake. In addition

Refined pipe theory for mechanistic modeling of wood development.

Science.gov (United States)

Deckmyn, Gaby; Evans, Sam P; Randle, Tim J

2006-06-01

We present a mechanistic model of wood tissue development in response to changes in competition, management and climate. The model is based on a refinement of the pipe theory, where the constant ratio between sapwood and leaf area (pipe theory) is replaced by a ratio between pipe conductivity and leaf area. Simulated pipe conductivity changes with age, stand density and climate in response to changes in allocation or pipe radius, or both. The central equation of the model, which calculates the ratio of carbon (C) allocated to leaves and pipes, can be parameterized to describe the contrasting stem conductivity behavior of different tree species: from constant stem conductivity (functional homeostasis hypothesis) to height-related reduction in stem conductivity with age (hydraulic limitation hypothesis). The model simulates the daily growth of pipes (vessels or tracheids), fibers and parenchyma as well as vessel size and simulates the wood density profile and the earlywood to latewood ratio from these data. Initial runs indicate the model yields realistic seasonal changes in pipe radius (decreasing pipe radius from spring to autumn) and wood density, as well as realistic differences associated with the competitive status of trees (denser wood in suppressed trees).

Peace Negotiations in the Third World: A Comparative Analysis

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Raúl Benítez Manaut

1995-01-01

Full Text Available In this article the negotiations and peace processes in the Third World are analized from a comparative viewpoint in order to focus in on the case of Centroamerica. Reference is made to the special features and common elements of those peace processes in otherregions of the Third World and they are compared to those which have taken place in Centroamerica. It is a retrospective and comparative analysis. For this reason, the author has decided to carry out a brief typology of those conflicts offered by Centroamerica: inNicaragua, El Salvador and Guatemala. Later, the author goes on to analyse the most relevant peace and negotiation processes involving the Third World including one or two from Latin America: the cases of Panama, Afghanistan, Iran-Iraq, Colombia, southern Africa (South Africa, Namibia and Angola and Cambodia. Later, the author goes overthe peace process periods in Centroamerica and the temporary contradictions which are presented by internal conflict, regional conflict and geopolitical conflict. Finally, a comparative methodological exercise is carried out which allows to focus on modes of implementation of the peace processes.

Mechanistic studies related to the safety of Li/SOCl2 cells

Science.gov (United States)

Carter, B. J.; Williams, R. M.; Tsay, F. D.; Rodriguez, A.; Kim, S.; Evans, M. M.; Frank, H.

1985-01-01

Mechanistic studies of the reactions in Li-SOCl2 cells have been undertaken to improve understanding of the safety problems of these cells. The electrochemical reduction of 1.5M LiAlCl4/SOCl2 has been investigated using gas chromatography, electron spin resonance spectroscopy, and infrared spectroscopy. Cl2 and S2Cl2 have been identified as intermediates in the reduction of SOCl2, along with a radical species (g/xx/ = 2.004, g/yy/ = 2.016, g/zz/ = 2.008) and the proposed triplet ground-state dimer of this radical. SO2 and sulfur have been identified as products. Based upon these findings, a mechanism for the electrochemical reduction of 1.5M LiAlCl4/SOCl2 has been proposed, and its implications for safety of Li-SOCl2 cells during discharge to +0.5V at 25-30 C are discussed.

Mechanistic study on spraying of blended biodiesel using phase Doppler anemometry

International Nuclear Information System (INIS)

Kamrak, Juthamas; Kongsombut, Benjapol; Grehan, Gerard; Saengkaew, Sawitree; Kim, Kyo-Seon; Charinpanitkul, Tawatchai

2009-01-01

Droplet size and dynamics of blended palm oil-based fatty acid methyl ester (FAME) and diesel oil spray were mechanistically investigated using a phase Doppler anemometry. A two-fluid atomizer was applied for dispersing viscous blends of blended biodiesel oil with designated flow rates. It was experimentally found that the atomizer could generate a spray with large droplets with Sauter mean diameters of ca. 30 μm at low air injection pressure. Such large droplets traveled with a low velocity along their trajectory after emerging from the nozzle tip. The viscosity of blended biodiesel could significantly affect the atomizing process, resulting in the controlled droplet size distribution. Blended biodiesel with a certain fraction of palm oil-based FAME would be consistently atomized owing to its low viscosity. However, the viscosity could exert only a small effect on the droplet velocity profile with the air injection pressure higher than 0.2 MPa.

A semi-mechanistic approach to calculate the probability of fuel defects

International Nuclear Information System (INIS)

Tayal, M.; Millen, E.; Sejnoha, R.

1992-10-01

In this paper the authors describe the status of a semi-mechanistic approach to the calculation of the probability of fuel defects. This approach expresses the defect probability in terms of fundamental parameters such as local stresses, local strains, and fission product concentration. The calculations of defect probability continue to reflect the influences of the conventional parameters like power ramp, burnup and CANLUB. In addition, the new approach provides a mechanism to account for the impacts of additional factors involving detailed fuel design and reactor operation, for example pellet density, pellet shape and size, sheath diameter and thickness, pellet/sheath clearance, and coolant temperature and pressure. The approach has been validated against a previous empirical correlation. AN illustrative example shows how the defect thresholds are influenced by changes in the internal design of the element and in the coolant pressure. (Author) (7 figs., tab., 12 refs.)

Mechanistic origin of dragon-kings in a population of competing agents

Science.gov (United States)

Johnson, N.; Tivnan, B.

2012-05-01

We analyze the mechanistic origins of the extreme behaviors that arise in an idealized model of a population of competing agents, such as traders in a market. These extreme behaviors exhibit the defining characteristics of `dragon-kings'. Our model comprises heterogeneous agents who repeatedly compete for some limited resource, making binary choices based on the strategies that they have in their possession. It generalizes the well-known Minority Game by allowing agents whose strategies have not made accurate recent predictions, to step out of the competition until their strategies improve. This generates a complex dynamical interplay between the number V of active agents (mimicking market volume) and the imbalance D between the decisions made (mimicking excess demand). The wide spectrum of extreme behaviors which emerge, helps to explain why no unique relationship has been identified between the price and volume during real market crashes and rallies.

Comparative analysis of prophages in Streptococcus mutans genomes

Science.gov (United States)

Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin

2017-01-01

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986

COMPARATIVE ANALYSIS OF INNOVATION ASPECT EVIDENCE IN CONSTRUCTION AND MULTI-SECTOR COMPANIES

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Ricardo Floriani

2010-12-01

Full Text Available The goal of this study is to make a comparative analysis of innovation aspect evidence among construction and multi-sector companies. Descriptive research was done through a content analysis of administration reports from 2005 to 2007. From the researched material, 14 aspects of innovations were extracted, which offer the basis to the content analysis. Two non-probability samples were developed, the first consisting of 22 multi-sector businesses, within 18 economic sectors, which comprises the companies in the comparison. Aspects of innovation found in this group of companies were compared to those stated in the reports of the administration of the 34 construction companies with open capital, which comprise the second sample. The survey results show that the evidence of innovation aspects are different in construction companies when compared to the administration reports of multi-sector business of 2005, 2006 and 2007. The construction companies state fewer innovation aspects in the administration reports than multisector companies in the analyzed period. The conclusion is that while construction companies can be considered fairly innovative, multi-sectorial companies present more innovations on average.

Comparative analysis of old, recycled and new PV modules

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Haroon Ashfaq

2017-01-01

Full Text Available This paper presents comparative analysis of old, recycled and new PV modules. It is possible to recycle even very old products by modern standard processes in a value-conserving manner. About 90% of the materials recovered from solar panels can be recycled into useful products. Carbon emission and energy cost are low in manufacturing recycled SPV. Modules can be manufactured with recycled materials and reinstalled in systems as a full quality product with today’s technology good for another 25–30 years. Analysis of all the models of PV module is done with the help of MATLAB. This helps in comparison and proves the effectiveness of the recycled PV module based systems.

Comparative Genomics and Transcriptomic Analysis of Mycobacterium Kansasii

KAUST Repository

Alzahid, Yara

2014-04-01

The group of Mycobacteria is one of the most intensively studied bacterial taxa, as they cause the two historical and worldwide known diseases: leprosy and tuberculosis. Mycobacteria not identified as tuberculosis or leprosy complex, have been referred to by ‘environmental mycobacteria’ or ‘Nontuberculous mycobacteria (NTM). Mycobacterium kansasii (M. kansasii) is one of the most frequent NTM pathogens, as it causes pulmonary disease in immuno-competent patients and pulmonary, and disseminated disease in patients with various immuno-deficiencies. There have been five documented subtypes of this bacterium, by different molecular typing methods, showing that type I causes tuberculosis-like disease in healthy individuals, and type II in immune-compromised individuals. The remaining types are said to be environmental, thereby, not causing any diseases. The aim of this project was to conduct a comparative genomic study of M. kansasii types I-V and investigating the gene expression level of those types. From various comparative genomics analysis, provided genomics evidence on why M. kansasii type I is considered pathogenic, by focusing on three key elements that are involved in virulence of Mycobacteria: ESX secretion system, Phospholipase c (plcb) and Mammalian cell entry (Mce) operons. The results showed the lack of the espA operon in types II-V, which renders the ESX- 1 operon dysfunctional, as espA is one of the key factors that control this secretion system. However, gene expression analysis showed this operon to be deleted in types II, III and IV. Furthermore, plcB was found to be truncated in types III and IV. Analysis of Mce operons (1-4) show that mce-1 operon is duplicated, mce-2 is absent and mce-3 and mce-4 is present in one copy in M. kansasii types I-V. Gene expression profiles of type I-IV, showed that the secreted proteins of ESX-1 were slightly upregulated in types II-IV when compared to type I and the secreted forms of ESX-5 were highly down

Mechanistic movement models to understand epidemic spread.

Science.gov (United States)

Fofana, Abdou Moutalab; Hurford, Amy

2017-05-05

An overlooked aspect of disease ecology is considering how and why animals come into contact with one and other resulting in disease transmission. Mathematical models of disease spread frequently assume mass-action transmission, justified by stating that susceptible and infectious hosts mix readily, and foregoing any detailed description of host movement. Numerous recent studies have recorded, analysed and modelled animal movement. These movement models describe how animals move with respect to resources, conspecifics and previous movement directions and have been used to understand the conditions for the occurrence and the spread of infectious diseases when hosts perform a type of movement. Here, we summarize the effect of the different types of movement on the threshold conditions for disease spread. We identify gaps in the literature and suggest several promising directions for future research. The mechanistic inclusion of movement in epidemic models may be beneficial for the following two reasons. Firstly, the estimation of the transmission coefficient in an epidemic model is possible because animal movement data can be used to estimate the rate of contacts between conspecifics. Secondly, unsuccessful transmission events, where a susceptible host contacts an infectious host but does not become infected can be quantified. Following an outbreak, this enables disease ecologists to identify 'near misses' and to explore possible alternative epidemic outcomes given shifts in ecological or immunological parameters.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Author(s).

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts

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Kim Sun

2008-03-01

Full Text Available Abstract Background Once a new genome is sequenced, one of the important questions is to determine the presence and absence of biological pathways. Analysis of biological pathways in a genome is a complicated task since a number of biological entities are involved in pathways and biological pathways in different organisms are not identical. Computational pathway identification and analysis thus involves a number of computational tools and databases and typically done in comparison with pathways in other organisms. This computational requirement is much beyond the capability of biologists, so information systems for reconstructing, annotating, and analyzing biological pathways are much needed. We introduce a new comparative pathway analysis workbench, ComPath, which integrates various resources and computational tools using an interactive spreadsheet-style web interface for reliable pathway analyses. Results ComPath allows users to compare biological pathways in multiple genomes using a spreadsheet style web interface where various sequence-based analysis can be performed either to compare enzymes (e.g. sequence clustering and pathways (e.g. pathway hole identification, to search a genome for de novo prediction of enzymes, or to annotate a genome in comparison with reference genomes of choice. To fill in pathway holes or make de novo enzyme predictions, multiple computational methods such as FASTA, Whole-HMM, CSR-HMM (a method of our own introduced in this paper, and PDB-domain search are integrated in ComPath. Our experiments show that FASTA and CSR-HMM search methods generally outperform Whole-HMM and PDB-domain search methods in terms of sensitivity, but FASTA search performs poorly in terms of specificity, detecting more false positive as E-value cutoff increases. Overall, CSR-HMM search method performs best in terms of both sensitivity and specificity. Gene neighborhood and pathway neighborhood (global network visualization tools can be used

Flow regimes and mechanistic modeling of critical heat flux under subcooled flow boiling conditions

Science.gov (United States)

Le Corre, Jean-Marie

Thermal performance of heat flux controlled boiling heat exchangers are usually limited by the Critical Heat Flux (CHF) above which the heat transfer degrades quickly, possibly leading to heater overheating and destruction. In an effort to better understand the phenomena, a literature review of CHF experimental visualizations under subcooled flow boiling conditions was performed and systematically analyzed. Three major types of CHF flow regimes were identified (bubbly, vapor clot and slug flow regime) and a CHF flow regime map was developed, based on a dimensional analysis of the phenomena and available data. It was found that for similar geometric characteristics and pressure, a Weber number (We)/thermodynamic quality (x) map can be used to predict the CHF flow regime. Based on the experimental observations and the review of the available CHF mechanistic models under subcooled flow boiling conditions, hypothetical CHF mechanisms were selected for each CHF flow regime, all based on a concept of wall dry spot overheating, rewetting prevention and subsequent dry spot spreading. It is postulated that a high local wall superheat occurs locally in a dry area of the heated wall, due to a cyclical event inherent to the considered CHF two-phase flow regime, preventing rewetting (Leidenfrost effect). The selected modeling concept has the potential to span the CHF conditions from highly subcooled bubbly flow to early stage of annular flow. A numerical model using a two-dimensional transient thermal analysis of the heater undergoing nucleation was developed to mechanistically predict CHF in the case of a bubbly flow regime. In this type of CHF two-phase flow regime, the high local wall superheat occurs underneath a nucleating bubble at the time of bubble departure. The model simulates the spatial and temporal heater temperature variations during nucleation at the wall, accounting for the stochastic nature of the boiling phenomena. The model has also the potential to evaluate

A Comparative Analysis of Three Unique Theories of Organizational Learning

Science.gov (United States)

Leavitt, Carol C.

2011-01-01

The purpose of this paper is to present three classical theories on organizational learning and conduct a comparative analysis that highlights their strengths, similarities, and differences. Two of the theories -- experiential learning theory and adaptive -- generative learning theory -- represent the thinking of the cognitive perspective, while…

Mechanistic insight into neurotoxicity induced by developmental insults

International Nuclear Information System (INIS)

Tamm, Christoffer; Ceccatelli, Sandra

2017-01-01

Epidemiological and/or experimental studies have shown that unfavorable prenatal environmental factors, such as stress or exposure to certain neurotoxic environmental contaminants, may have adverse consequences for neurodevelopment. Alterations in neurogenesis can have harmful effects not only for the developing nervous system, but also for the adult brain where neurogenesis is believed to play a role in learning, memory, and even in depression. Many recent advances in the understanding of the complex process of nervous system development can be integrated into the field of neurotoxicology. In the past 15 years we have been using cultured neural stem or progenitor cells to investigate the effects of neurotoxic stimuli on cell survival, proliferation and differentiation, with special focus on heritable effects. This is an overview of the work performed by our group in the attempt to elucidate the mechanisms of developmental neurotoxicity and possibly provide relevant information for the understanding of the etiopathogenesis of complex brain disorders. - Highlights: • The developing nervous system is highly sensitive to toxic insults. • Neural stem cells are relevant models for mechanistic studies as well as for identifying heritable effects due to epigenetic changes. • Depending on the dose, the outcome of exposure to neurotoxicants ranges from altered proliferation and differentiation to cell death. • The elucidation of neurotoxicity mechanisms is relevant for understanding the etiopathogenesis of developmental and adult nervous system disorders.

Multiscale mechanistic modeling in pharmaceutical research and development.

Science.gov (United States)

Kuepfer, Lars; Lippert, Jörg; Eissing, Thomas

2012-01-01

Discontinuation of drug development projects due to lack of efficacy or adverse events is one of the main cost drivers in pharmaceutical research and development (R&D). Investments have to be written-off and contribute to the total costs of a successful drug candidate receiving marketing authorization and allowing return on invest. A vital risk for pharmaceutical innovator companies is late stage clinical failure since costs for individual clinical trials may exceed the one billion Euro threshold. To guide investment decisions and to safeguard maximum medical benefit and safety for patients recruited in clinical trials, it is therefore essential to understand the clinical consequences of all information and data generated. The complexity of the physiological and pathophysiological processes and the sheer amount of information available overcharge the mental capacity of any human being and prevent a prediction of the success in clinical development. A rigorous integration of knowledge, assumption, and experimental data into computational models promises a significant improvement of the rationalization of decision making in pharmaceutical industry. We here give an overview of the current status of modeling and simulation in pharmaceutical R&D and outline the perspectives of more recent developments in mechanistic modeling. Specific modeling approaches for different biological scales ranging from intracellular processes to whole organism physiology are introduced and an example for integrative multiscale modeling of therapeutic efficiency in clinical oncology trials is showcased.

Analytical techniques for mechanistic characterization of EUV photoresists

Science.gov (United States)

Grzeskowiak, Steven; Narasimhan, Amrit; Murphy, Michael; Ackerman, Christian; Kaminsky, Jake; Brainard, Robert L.; Denbeaux, Greg

2017-03-01

Extreme ultraviolet (EUV, 13.5 nm) lithography is the prospective technology for high volume manufacturing by the microelectronics industry. Significant strides towards achieving adequate EUV source power and availability have been made recently, but a limited rate of improvement in photoresist performance still delays the implementation of EUV. Many fundamental questions remain to be answered about the exposure mechanisms of even the relatively well understood chemically amplified EUV photoresists. Moreover, several groups around the world are developing revolutionary metal-based resists whose EUV exposure mechanisms are even less understood. Here, we describe several evaluation techniques to help elucidate mechanistic details of EUV exposure mechanisms of chemically amplified and metal-based resists. EUV absorption coefficients are determined experimentally by measuring the transmission through a resist coated on a silicon nitride membrane. Photochemistry can be evaluated by monitoring small outgassing reaction products to provide insight into photoacid generator or metal-based resist reactivity. Spectroscopic techniques such as thin-film Fourier transform infrared (FTIR) spectroscopy can measure the chemical state of a photoresist system pre- and post-EUV exposure. Additionally, electrolysis can be used to study the interaction between photoresist components and low energy electrons. Collectively, these techniques improve our current understanding of photomechanisms for several EUV photoresist systems, which is needed to develop new, better performing materials needed for high volume manufacturing.

Using yield gap analysis to give sustainable intensification local meaning

NARCIS (Netherlands)

Silva, João Vasco

2017-01-01

Yield gap analysis is useful to understand the relative contribution of growth-defining, -limiting and -reducing factors to actual yields. This is traditionally performed at the field level using mechanistic crop growth simulation models, and directly up-scaled to the regional and global levels

Synthesis, Photoluminescence Behavior of Green Light Emitting Tb(III) Complexes and Mechanistic Investigation of Energy Transfer Process.

Science.gov (United States)

Bala, Manju; Kumar, Satish; Devi, Rekha; Khatkar, Avni; Taxak, V B; Boora, Priti; Khatkar, S P

2018-06-04

A series of five new terbium(III) ion complexes with 4,4-difluoro-1-phenylbutane-1,3-dione (HDPBD) and anciliary ligands was synthesized. The composition and properties of complexes were analyzed by elemental analysis, IR, NMR, powder X-ray diffaraction, TG-DTG and photoluminescence spectroscopy. These complexes exhibited ligand sensitized green emission at 546 nm associated with 5 D 4  →  7 F 5 transitions of terbium ion in the emission spectra. The photoluminescence study manifested that the organic ligands act as antenna and facilitate the absorbed energy to emitting levels of Tb(III) ion efficiently. The enhanced luminescence intensity and decay time of ternary C2-C5 complexes observed due to synergistic effect of anciliary ligands. The CIE color coordinates of complexes came under the green region of chromaticity diagram. The mechanistic investigation of intramolecular energy transfer in the complexes was discussed in detail. These terbium(III) complexes can be thrivingly used as one of the green component in light emitting material and in display devices. Graphical Abstract Illustrate the sensitization process of the Tb ion and intramolecular energy transfer process in the Tb 3+ complex.

Mechanistic Basis for Plant Responses to Drought Stress : Regulatory Mechanism of Abscisic Acid Signaling

Science.gov (United States)

Miyakawa, Takuya; Tanokura, Masaru

The phytohormone abscisic acid (ABA) plays a key role in the rapid adaptation of plants to environmental stresses such as drought and high salinity. Accumulated ABA in plant cells promotes stomatal closure in guard cells and transcription of stress-tolerant genes. Our understanding of ABA responses dramatically improved by the discovery of both PYR/PYL/RCAR as a soluble ABA receptor and inhibitory complex of a protein phospatase PP2C and a protein kinase SnRK2. Moreover, several structural analyses of PYR/PYL/RCAR revealed the mechanistic basis for the regulatory mechanism of ABA signaling, which provides a rational framework for the design of alternative agonists in future.

A comparative analysis of protected area planning and management frameworks

Science.gov (United States)

Per Nilsen; Grant Tayler

1997-01-01

A comparative analysis of the Recreation Opportunity Spectrum (ROS), Limits of Acceptable Change (LAC), a Process for Visitor Impact Management (VIM), Visitor Experience and Resource Protection (VERP), and the Management Process for Visitor Activities (known as VAMP) decision frameworks examines their origins; methodology; use of factors, indicators, and standards;...

A comparative analysis of Piezoelectric and Magnetostrictive actuators in Smart Structures

OpenAIRE

Pons Rovira, José Luis

2005-01-01

[EN] This paper introduces a comparative analysis of Piezoelectric (PZ) and Magnetostrictive (MS) actuators as components in smart structures. There is an increasing interest in functional structures which are able to adapt to external or internal perturbations, i.e. changes in loading conditions or ageing. Actuator technologies must perform concomitantly as sensors and actuators to be applicable in smart structures. In this paper we will comparatively analyze the possibility of usin...

Dimeric spectra analysis in Microsoft Excel: a comparative study.

Science.gov (United States)

Gilani, A Ghanadzadeh; Moghadam, M; Zakerhamidi, M S

2011-11-01

The purpose of this work is to introduce the reader to an Add-in implementation, Decom. This implementation provides the whole processing requirements for analysis of dimeric spectra. General linear and nonlinear decomposition algorithms were integrated as an Excel Add-in for easy installation and usage. In this work, the results of several samples investigations were compared to those obtained by Datan. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

CONPAS 1.0 (CONtainment Performance Analysis System). User`s manual

Energy Technology Data Exchange (ETDEWEB)

Ahn, Kwang Il; Jin, Young Ho [Korea Atomic Energy Research Institute, Daeduk (Korea, Republic of)

1996-04-01

CONPAS (CONtainment Performance Analysis System) is a verified computer code package to integrate the numerical, graphical, and results-operation aspects of Level 2 probabilistic safety assessments (PSA) for nuclear power plants automatically under a PC window environment. Compared with the existing DOS-based computer codes for Level 2 PSA, the most important merit of the window-based computer code is that user can easily describe and quantify the accident progression models, and manipulate the resultant outputs in a variety of ways. As a main logic for accident progression analysis, CONPAS employs a concept of the small containment phenomenological event tree (CPET) helpful to trace out visually individual accident progressions and of the large supporting event tree (LSET) for its detailed quantification. For the integrated analysis of Level 2 PSA, the code utilizes four distinct, but closely related modules; (1) ET Editor for construction of several event tree models describing the accident progressions, (2) Computer for quantification of the constructed event trees and graphical display of the resultant outputs, (3) Text Editor for preparation of input decks for quanification and utilization of calculational results, and (4) Mechanistic Code Plotter for utilization of results obtained from severe accident analysis codes. Compared with other existing computer codes for Level 2 PSA, the CONPAS code provides several advanced features: computational aspects including systematic uncertainty analysis, importance analysis, sensitivity analysis and data interpretation, reporting aspects including tabling and graphic as well as user-friend interface. 10 refs. (Author) .new.

Toward a mechanistic modeling of nitrogen limitation for photosynthesis

Science.gov (United States)

Xu, C.; Fisher, R. A.; Travis, B. J.; Wilson, C. J.; McDowell, N. G.

2011-12-01

The nitrogen limitation is an important regulator for vegetation growth and global carbon cycle. Most current ecosystem process models simulate nitrogen effects on photosynthesis based on a prescribed relationship between leaf nitrogen and photosynthesis; however, there is a large amount of variability in this relationship with different light, temperature, nitrogen availability and CO2 conditions, which can affect the reliability of photosynthesis prediction under future climate conditions. To account for the variability in nitrogen-photosynthesis relationship under different environmental conditions, in this study, we developed a mechanistic model of nitrogen limitation for photosynthesis based on nitrogen trade-offs among light absorption, electron transport, carboxylization and carbon sink. Our model shows that strategies of nitrogen storage allocation as determined by tradeoff among growth and persistence is a key factor contributing to the variability in relationship between leaf nitrogen and photosynthesis. Nitrogen fertilization substantially increases the proportion of nitrogen in storage for coniferous trees but much less for deciduous trees, suggesting that coniferous trees allocate more nitrogen toward persistence compared to deciduous trees. The CO2 fertilization will cause lower nitrogen allocation for carboxylization but higher nitrogen allocation for storage, which leads to a weaker relationship between leaf nitrogen and maximum photosynthesis rate. Lower radiation will cause higher nitrogen allocation for light absorption and electron transport but less nitrogen allocation for carboxylyzation and storage, which also leads to weaker relationship between leaf nitrogen and maximum photosynthesis rate. At the same time, lower growing temperature will cause higher nitrogen allocation for carboxylyzation but lower allocation for light absorption, electron transport and storage, which leads to a stronger relationship between leaf nitrogen and maximum

Comparative thermal buckling analysis of functionally graded plate

Directory of Open Access Journals (Sweden)

Čukanović Dragan V.

2017-01-01

Full Text Available A thermal buckling analysis of functionally graded thick rectangular plates accord¬ing to von Karman non-linear theory is presented. The material properties of the functionally graded plate, except for the Poisson’s ratio, were assumed to be graded in the thickness direction, according to a power-law distribution, in terms of the volume fractions of the metal and ceramic constituents. Formulations of equilibrium and stability equations are derived using the high order shear deformation theory based on different types of shape functions. Analytical method for determination of the critical buckling temperature for uniform increase of temperature, linear and non-linear change of temperature across thickness of a plate is developed. Numeri¬cal results were obtained in МATLAB software using combinations of symbolic and numeric values. The paper presents comparative results of critical buckling tempera¬ture for different types of shape functions. The accuracy of the formulation presented is verified by comparing to results available from the literature.

Mechanistic investigation on microbial toxicity of nano hydroxyapatite on implant associated pathogens

Energy Technology Data Exchange (ETDEWEB)

Baskar, K. [Department of Biotechnology, University of Madras, Guindy Campus, Chennai, Tamil Nadu (India); Anusuya, T. [Department of Nanotechnology, SRM University, Kattankulathur, Tamil Nadu (India); Devanand Venkatasubbu, G., E-mail: gdevanandvenkatasubbu@gmail.com [Department of Nanotechnology, SRM University, Kattankulathur, Tamil Nadu (India)

2017-04-01

The use of atomic scale inorganic nanoparticles (NPs) to fight against pathogenic microorganisms is a recent trend in biomedical area which overcomes the limitations of organic compounds in terms of stability, shelf life and bioactivity. One such Calcium phosphate based biomaterial is hydroxyapatite (HA), considered as potential bioactive compound with excellent biocompatibility, osteointegrity and biodegradability. Osteomyelitis, the implant associated infection, is the major problem worldwide responsible for the majority of implant failure cases. Since HA is used as a coating material of implants, only few reports were available on its antimicrobial activity and cytotoxicity whereas no reports on its possible antimicrobial mechanism. In this present study, the HA-NPs were synthesized by wet chemical precipitation and were characterized using X-ray diffraction (XRD), Transmission Electron Microscopy (TEM) and Fourier transform infrared spectroscopy (FTIR). The synthesized HA-NPs were evaluated for antimicrobial activity against implant associated bacterial pathogens. The study also explores the mechanistic action of HA-NPs in killing of bacteria by determining the reactive oxygen species (ROS) generation, DNA fragmentation, Lactate dehydrogenase (LDH) leakage and cellular interaction. In addition the cytotoxicity of HA-NPs was determined by MTT assay and Fluorescence Microscopic analysis. The results revealed that, the synthesized HA-NPs showed good antibacterial activity for tested bacterial species and the possible antibacterial mechanism were due to the lack of membrane integrity and cytotoxic studies shows the concentration dependent changes in cell viability. - Highlights: • Antibacterial activity against Gram − ve bacterium • Mechanism of antibacterial activity is analyzed. • DNA fragmentation, growth curve, LDH, ROS are analyzed. • The mechanism is by damaging cell membrane. • Hydroxyapatite is biocompatible.

In vitro solubility, dissolution and permeability studies combined with semi-mechanistic modeling to investigate the intestinal absorption of desvenlafaxine from an immediate- and extended release formulation.

Science.gov (United States)

Franek, F; Jarlfors, A; Larsen, F; Holm, P; Steffansen, B

2015-09-18

Desvenlafaxine is a biopharmaceutics classification system (BCS) class 1 (high solubility, high permeability) and biopharmaceutical drug disposition classification system (BDDCS) class 3, (high solubility, poor metabolism; implying low permeability) compound. Thus the rate-limiting step for desvenlafaxine absorption (i.e. intestinal dissolution or permeation) is not fully clarified. The aim of this study was to investigate whether dissolution and/or intestinal permeability rate-limit desvenlafaxine absorption from an immediate-release formulation (IRF) and Pristiq(®), an extended release formulation (ERF). Semi-mechanistic models of desvenlafaxine were built (using SimCyp(®)) by combining in vitro data on dissolution and permeation (mechanistic part of model) with clinical data (obtained from literature) on distribution and clearance (non-mechanistic part of model). The model predictions of desvenlafaxine pharmacokinetics after IRF and ERF administration were compared with published clinical data from 14 trials. Desvenlafaxine in vivo dissolution from the IRF and ERF was predicted from in vitro solubility studies and biorelevant dissolution studies (using the USP3 dissolution apparatus), respectively. Desvenlafaxine apparent permeability (Papp) at varying apical pH was investigated using the Caco-2 cell line and extrapolated to effective intestinal permeability (Peff) in human duodenum, jejunum, ileum and colon. Desvenlafaxine pKa-values and octanol-water partition coefficients (Do:w) were determined experimentally. Due to predicted rapid dissolution after IRF administration, desvenlafaxine was predicted to be available for permeation in the duodenum. Desvenlafaxine Do:w and Papp increased approximately 13-fold when increasing apical pH from 5.5 to 7.4. Desvenlafaxine Peff thus increased with pH down the small intestine. Consequently, desvenlafaxine absorption from an IRF appears rate-limited by low Peff in the upper small intestine, which "delays" the predicted

A comparative analysis of national food recall systems

Directory of Open Access Journals (Sweden)

Gaetano Liuzzo

2013-12-01

Full Text Available Food recall and withdrawal is a fundamental tool for risk management and different countries stated the mandatory application of a system for food; the present work is an analysis of different systems applied in different countries. The main objective of analysed systems is the consumer’s health protection through an audit system and the application of system to rapidly recall/withdraw food on the part of producers. The comparative analysis of different national systems [i.e. European Union (EU, Australia, Canada, US and China] shows differences both of the terminological and legal aspects; the words recall and withdrawal have different meaning in EU legislation than in other counties’ legislations; from a legal point of view, two main recall/withdrawal systems could be identified: a mandatory one (EU and China and a voluntary one (USA, Canada and Australia; all the investigated systems have a co-operative approach between authority and food business operator, but different functions on their respective roles could be identified.

Title: A Comparative Analysis of Nursing Education and other forms of

African Journals Online (AJOL)

DR. MRS. AKPABIO

A COMPARATIVE ANALYSIS OF NURSING EDUCATION. AND OTHER ... As a dynamic service oriented profession .... Technology, in line with nursing had come a long way from the .... prominence in future deliberations aimed at improving ...

Hawaiian propolis: comparative analysis and botanical origin.

Science.gov (United States)

Inui, Saori; Hosoya, Takahiro; Kumazaw, Shigenori

2014-02-01

Propolis is a resinous mixture of substances collected and processed from various botanical sources by honeybees (Apis mellifera). We recently obtained Hawaiian propolis, the study of which, to our knowledge, has not been reported. The purpose of this study was to analyze the composition of Hawaiian propolis and to identify its botanical origin. A comparative analysis of Hawaiian and Okinawan propolis and of the glandular trichomes on Macaranga tanarius fruit (the botanical origin of Okinawan propolis) was performed using reversed-phase high-performance liquid chromatography coupled with high resolution-electrospray mass spectrometry. Hawaiian propolis contained nine prenylflavonoids that were also isolated from Okinawan propolis. In conclusion, we suggest that the botanical origin of Hawaiian propolis is M. tanarius, the same as that of Okinawan propolis.